Endophytic microbial symbionts in plant prenatal care

ABSTRACT

The present disclosure provides novel endophyte strains or cultures thereof that have a symbiotic relationship with plants. The present disclosure further provides methods of improving seed vitality, biotic and abiotic stress resistance, plant health and yield under both stressed and unstressed environmental conditions, comprising inoculating a seed with the novel endophyte strains and cultivating a plant therefrom.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is the National Stage of International Application No. PCT/CA2013/000091, filed Feb. 5, 2013, which is herein incorporated in its entirety by reference.

SEQUENCE LISTING

The instant application contains a Sequence Listing with 19 sequences which was submitted via EFS-Web on Aug. 5, 2015 and incorporated by reference in its entirety. Said ASCII copy, created on Aug. 5, 2015 is named 30078US_CRF_sequencelisting.txt, and is 9675 bytes in size.

FIELD

The present disclosure relates to fungal and bacterial endophytes of plants that enhance seed vitality and/or plant health, conferring general improvements in the plant's agricultural traits, under normal and stressed conditions. The disclosure also relates to these isolated endophytes.

BACKGROUND

Fungi and bacteria are ubiquitous microorganisms. Endophyte is the term first coined by de Bary [1866] defining those microbes that colonize asymptomatically plant tissues [Stone et al., 2000]. The existence of endophytes has been known for more than one century [Freeman 1904] and it seems that each individual host, among the 300,000 plant species, inhabits several to hundreds of endophytes [Tan and Zou, 2001]. Endophytes are microbial organisms mostly symbiotically or mutualistically associated with living tissues of plant hosts. Many are capable of conferring plant tolerance to abiotic stressors or can be used by the plant for defense against pathogenic fungi and bacteria [Singh et al. 2011]. Some of these microorganisms have proven useful for agriculture, forestry and horticulture sectors, as well as plant production of medicinally important compounds.

Endophytes largely determine plant cell and whole plant genome regulation, including plant's vital cycles: (i) seed pre- and post-germination events (mycovitalism) [Vujanovic and Vujanovic 2007], (ii) plant nutrient uptake and growth-promoting mechanisms (mycoheterotrophism) [Smith and Read 2008], and (iii) plant environmental stress tolerance and induced systemic resistance against diseases and pests (mycosymbionticism) [Wallin 1927; Margulis, 1991]. They could play a major role in plant biomass production, CO₂ sequestration, and/or yield and therefore be significant players in regulating the ecosphere, ensuring plant health and food security. In addition, they can be important sentinels (bioindicators) of environmental changes, as alterations in the structure and biomass of endophytic communities can herald changes not only in pathways of nutrient (N, P, K), energy transfer in food-webs and biogeochemical cycles but also in UV-B, heat, drought or salt tolerance influencing the overall plant ecosystem establishment and stability. Despite their abundance and likely importance in all terrestrial ecosystems, nearly nothing about the composition of endophytes in seeds or spermosphere, their interactions, or their common response to environmental changes is known.

While the spermosphere represents a rapidly changing and microbiologically dynamic zone of soil surrounding a germinating seed [Nelson, 2004], the rhizosphere is a microbiologically active zone of the bulk soil surrounding the plant's roots [Smith and Read 2008]. The rhizosphere supports mycoheterotrophy or a plant-mycorrhiza symbiotic relationship. The spermosphere, on the other hand, promotes mycovitality or an endophytic fungi relationship with the plant seeds—enhancing seed vigour, energy and uniformity of germination that could be fairly predicted. Fungal endophytes are distinct from mycorrhizae in that they can colonize not only roots, but also other plant organs including seeds [Vujanovic et al. 2000; Hubbard et al. 2011]. They belong to the multicellular phyla Ascomycota and Basidiomycota and form colonization symbiotic structures different from those produced by unicellular or cenocytic phylum Glomeromycota, known as vesicular-arbuscular mycorrhizal symbiosis [Abdellatif et al. 2009]. Endophytic bacteria have been also found in virtually every plant studied, where they colonize an ecological niche similar to that of fungi, such as the internal healthy tissues. Although most bacterial endophytes appear to originate from the rhizosphere or phyllosphere; some may be transmitted through the seed [Ryan et al. 2008].

Seed germination is a vital phenophase to plants' survival and reproduction in either optimal or stressful environmental conditions. Microbial endophytic colonization at the seed state is especially critical because of the role of the seed as a generative organ in regeneration and dispersion of flowering plants [Baskin and Baskin 2004] and the role of mycobionts and symbiotically associated bacteria (bactobionts) as potential drivers of seedling recruitment in natural—undisturbed, disturbed and polluted—habitats [Mühlmann and Peintner 2000; Adriaensen et al. 2006; White and Torres 2010]. Thus, developing methods by which seedling emergence can be enhanced and protected under the limitations of disease pressure, heat or drought is precious. The use of endophytic symbionts is a promising method by which seed germination can be enhanced [Vujanovic et al. 2000; Vujanovic and Vujanovic 2006; Vujanovic and Vujanovic 2007]. It was hypothesized that plant stress hardiness can be conferred via a mycobiont-seed relationship known as mycovitality—a phenomenon that had been reserved for Orchidaceae [Vujanovic 2008] and via bactovitality which refers to a form of bactosymbiosis, using different endophytic strains with variety of activities.

SUMMARY

Endophytes can benefit plant hosts such as wheat, barley, pulses, canola, tree, shrub or grass in a variety of ways, including bactovitality, mycovitality and mycoheterotrophy, and enhanced tolerance to environmental stresses, as demonstrated herein. Prenatal care in agriculture, as demonstrated herein with six endophytic strains, is more than just seed or germinant vitality, health or vigour. It also determines what to expect before and during the germination process, seedling establishment, and, later crop productivity or yield.

Several parameters of symbiotic efficacy (dormancy breakdown, germination, growth and yield) were assessed using efficient endophytic Saskatchewan Microbial Collection and Database (SMCD) strain(s)-crop(s) interaction(s) under in vitro, phytotron, greenhouse and field conditions.

Also tested was the bacterial endophyte capacity to confer seed vitality. For both fungal and bacterial endosymbionts, improved seed vitality can increase tolerance for abiotic and biotic stresses in plants that have progressed beyond the seedling stage to the plant's maturity via mycoheterotrophy.

Accordingly, the present disclosure provides an isolated endophyte of Streptomyces sp. strain or culture thereof which is deposited under the International Depositary Authority of Canada (IDAC, National Microbiology Laboratory. Public Health Agency of Canada. 1015 Arlington Street, Winnipeg, Manitoba, Canada, R3E 3R2) accession number 081111-06 or which comprises the 16S rDNA sequence as shown in SEQ ID NO:6; an isolated endophyte of Paraconyothirium sp. strain or culture thereof which is deposited as IDAC accession number 081111-03 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:5; an isolated endophyte of Pseudeurotium sp. or culture thereof which is deposited under IDAC accession number 081111-02 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:4; an isolated endophyte of Penicillium sp. or culture thereof which is deposited under IDAC accession number 081111-01 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:3; an isolated culture of Cladosporium sp. which is deposited under IDAC accession number 200312-06 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:1, and/or an isolated endophyte of Cladosporium sp. or culture thereof which is deposited under IDAC accession number 200312-05 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:2.

Also provided herein is a composition comprising an isolated endophyte or culture disclosed herein or a combination or mixture thereof and a carrier.

Further provided herein is a seed comprising an endophyte or culture disclosed herein. In one embodiment, the seed is coated with the endophyte. In another embodiment, the seed is cultured or planted near the endophyte such that the endophyte is able to colonize the seed.

The present disclosure also provides methods for improving seed vitality and enhancing plant health and yield under normal and stressed conditions. Accordingly, there is provided a method of improving seed vitality, plant health and/or plant yield comprising inoculating a seed with an endophyte or culture disclosed herein or a combination or mixture thereof or with a composition disclosed herein; and cultivating the seed into a first generation plant.

In one embodiment, the method comprises inoculating the seed with an isolated endophyte or culture thereof of Streptomyces sp. strain which is deposited under IDAC 081111-06 or which comprises the 16S rDNA sequence as shown in SEQ ID NO:6. In an embodiment, the method increases seed germination, decreases time to reach energy of germination, reduces hydrothermal time required for germination, increases seed germination vigour, increases the fresh weight of seedlings, enhances Rhizobium activity and nodulation frequency, and/or increases the yield of seedlings. In another embodiment, the method comprises reducing the effects of stress, such as drought, heat and/or biotic stress, such as Fusarium infection.

In another embodiment, the method comprises inoculating the seed with an isolated endophyte or culture thereof of Paraconyothirium sp. strain which is deposited as IDAC 081111-03 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:5. In an embodiment, the method increases seed germination, decreases time to reach energy of germination, reduces hydrothermal time required for germination, increases seed germination vigour, increases the fresh weight of seedlings and/or increases yield of seedlings. In another embodiment, the method comprises reducing the effects of stress, such as drought, heat and/or biotic stress, such as Fusarium infection.

In yet another embodiment, the method comprises inoculating the seed with an isolated endophyte or culture thereof of Pseudeurotium sp. which is deposited under IDAC 081111-02 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:4. In an embodiment, the method decreases time to reach energy of germination, reduces hydrothermal time required for germination, increases seed germination vigour, and/or increases the fresh weight of seedlings. In another embodiment, the method comprises reducing the effects of stress, such as drought and/or heat stress.

In a further embodiment, the method comprises inoculating the seed with an isolated endophyte or culture thereof of Penicillium sp. which is deposited under IDAC 081111-01 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:3. In an embodiment, the method increases seed germination, decreases time to reach energy of germination, reduces hydrothermal time required for germination, increases seed germination vigour, and/or increases yield of seedlings. In another embodiment, the method comprises enhancing stratification, breaking dormancy and increasing stress resistance by modulating hormonal ent-kaurenoic (KAO), repression of shoot growth (RSG), abscisic acid (ABA), gibberellic acid GA, 14-3-3 or nitric oxide (NO) genes and/or stress resistance superoxide dismutase (SOD), manganese SOD (MnSOD), proline (Pro) or MYB genes expressions, reducing the effects of stress, such as drought, heat and/or biotic stress, such as Fusarium infection.

In yet a further embodiment, the method comprises inoculating the seed with an isolated endophyte or culture thereof of Cladosporium sp. which is deposited under IDAC 200312-06 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:1. In an embodiment, the method decreases time to reach energy of germination, reduces hydrothermal time required for germination, increases seed germination vigour, and/or increases the fresh weight of seedlings. In an embodiment, the method comprises reducing the effects of stress, such as drought and/or heat.

In yet another further embodiment, the method comprises inoculating the seed with an isolated endophyte or culture thereof of Cladosporium sp. which is deposited under IDAC 200312-05 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:2. In an embodiment, the method comprises reducing the effects of stress, such as drought and/or heat stress.

In an embodiment, the seed is coated with the endophyte, cultured with the endophyte or planted near the endophyte. In a particular embodiment, the seed planted near the endophyte is about 4 cm away from the endophyte.

The plant may be any plant. In one embodiment, the plant is a cereal (wheat or barley), pulse (pea, lentil or chickpea), flax, canola plant, coniferous tree (spruce or pine), broadleaf tree (willow or poplar), shrub (caragana or winterfat) or grass (fescue or wildrye).

In another aspect, there is provided a method of improving plant health and/or plant yield comprising treating plant propagation material or a plant with an endophyte or culture disclosed herein or a combination or mixture thereof or a composition disclosed herein; and cultivating the plant propagation material into a first generation plant or allowing the plant to grow.

In an embodiment, the plant propagation material is any plant generative/sexual (seed, generative bud or flower) and vegetative/asexual (stem, cutting, root, bulb, rhizome, tuber, vegetative bud, or leaf) part that has the ability to be cultivated into a new plant.

In an embodiment, the isolated endophyte or culture thereof is an isolated endophyte of Streptomyces sp. strain or culture thereof which is deposited under the International Depositary Authority of Canada (IDAC, National Microbiology Laboratory. Public Health Agency of Canada. 1015 Arlington Street, Winnipeg, Manitoba, Canada, R3E 3R2) accession number 081111-06 or which comprises the 16S rDNA sequence as shown in SEQ ID NO:6; an isolated endophyte of Paraconyothirium sp. strain or culture thereof which is deposited as IDAC accession number 081111-03 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:5; an isolated endophyte of Pseudeurotium sp. or culture thereof which is deposited under IDAC accession number 081111-02 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:4; an isolated endophyte of Penicillium sp. or culture thereof which is deposited under IDAC accession number 081111-01 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:3; an isolated culture of Cladosporium sp. which is deposited under IDAC accession number 200312-06 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:1, and/or an isolated endophyte of Cladosporium sp. or culture thereof which is deposited under IDAC accession number 200312-05 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:2.

In an embodiment, the methods enhance landscape development and remediation. Accordingly, in one embodiment, there is provided a method of reducing soil contamination comprising treating plant propagation material or a plant with an endophyte or culture disclosed herein or a combination or mixture thereof or a composition disclosed herein; and cultivating the plant propagation material into a first generation plant or allowing the plant to grow. In one embodiment, the soil contaminant is hydrocarbons, petroleum or other chemicals, salts, or metals, such as lead, cadmium or radioisotopes.

In another embodiment, the methods reduce the effects of stress, such as heat, drought and/or biotic stress.

The plant may be any plant. In one embodiment, the plant is a cereal (wheat and barley), pulse (pea, lentil or chickpea), flax, canola plant, coniferous tree (spruce or pine), broadleaf tree (willow or poplar), shrub (caragana or winterfat) or grass (fescue or wild rye).

Other features and advantages of the present disclosure will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples while indicating embodiments of the disclosure are given by way of illustration only, since various changes and modifications within the spirit and scope of the disclosure will become apparent to those skilled in the art from this detailed description and respective drawings and drawing legends.

BRIEF DESCRIPTION OF THE DRAWINGS

The disclosure will now be described in relation to the drawings in which:

FIG. 1 shows the phenotypic appearance of the endophytic fungal strains SMCD 2204, 2004F, 2206, 2208, and 2210 and bacterial strain SMCD 2215; after 10 days of growth on PDA at 21° C.

FIG. 2 shows the inferred neighbour-joining phylogenetic tree of the Cladosporium spp. SMCD 2204 and SMCD 2204F based on ITS rDNA. Numbers at nodes indicate bootstrap support values for 1000 replicates; only values that were >70% are given. Bar indicates 0.01 nucleotide substitutions per site (nucleotide position).

FIG. 3 shows the inferred neighbour-joining phylogenetic tree of the Penicillium sp. SMCD 2206 based on ITS rDNA. Numbers at nodes indicate bootstrap support values for 1000 replicates; only values that were >70% are given. Bar indicates 0.01 nucleotide substitutions per site (nucleotide position).

FIG. 4 shows the inferred neighbour-joining phylogenetic tree of the Pseudeurotium sp. SMCD 2208 based on ITS rDNA. Numbers at nodes indicate bootstrap support values for 1000 replicates; only values that were >70% are given. Bar indicates 0.01 nucleotide substitutions per site (nucleotide position).

FIG. 5 shows the inferred neighbour-joining phylogenetic tree of the Coniothyrium strain SMCD 2210 based on ITS rDNA. Numbers at nodes indicate bootstrap support values for 1000 replicates; only values that were >70% are given. Bar indicates 0.05 nucleotide substitutions per site (nucleotide position).

FIG. 6 shows the inferred neighbour-joining phylogenetic tree of the Streptomyces sp strain SMCD 2215 based on 16S rDNA. Numbers at nodes indicate bootstrap support values for 1000 replicates; only values that were >60% are given. Bar indicates 0.05 nucleotide substitutions per site (nucleotide position).

FIG. 7 shows left compartments of split plates (plant with microbial partner): healthy phenotypic appearance of wheat when the root is grown in contact with the microbial mats; and right-compartments of split plates (plant without microbial partner): massive formation of root hairs of wheat due to the plant-fungus association made in the left compartments of the split plates.

FIGS. 8 (A) and (C) shows SMCD2206 discontinuous colonization of wheat root (epidermis and cortex) tissue compared to (B) and (D) which shows pathogenic Fusarium graminearum's uniform/continual cell colonization of wheat root including vascular cylinder.

FIG. 9 shows keg index—level of deviation (irregularity) in endophyte (SMCDs) cell form.

FIG. 10 shows Idir index—level of direction changes when colonizing living plant-host cell.

FIG. 11 shows endophytic hyphae in root of wheat germinant (A—SMCD 2204; B—SMCD 2206; C—SMCD 2210; and D—SMCD-2215) visualized with lactofuchsin staining and fluorescence microscopy. Symbiotic structures/organs: (D) SMCD 2215 bacterial endophyte mostly formed curly intercellular filaments, whereas endophytic fungi (Figures to the right) produced: SMCD 2204 intracellular coils and arbuscules, SMCD 2206 intracellular vesicules, and SMCD 2110 intracellular knots.

FIG. 12 shows the appearance of symbiotic germinating wheat seedlings after 10 days on moist filter paper at 21° C.

FIG. 13 shows leaf length of germinating wheat seedlings after 10 days at moisture filter paper at 21° C.

FIG. 14 shows an in vitro inoculation method (A). A 5 mm² agar plug, cut from the margin of the parent colony, was placed hyphal side down in the centre of a 60 mm Petri dish containing potato dextrose agar (PDA) media. Next, five surface-sterilized seeds were placed a distance equivalent to 48 h hyphal growth from the agar plug and germinated in the dark. The impact of three seed surface sterilization methods on seed germination (B). Bars labeled with one or two asterisks (*) are significantly, or highly significantly, different from the same endophyte grown under control conditions (p≤0.05 or p≤0.01, respectively; ANOVA, followed by post-hoc LSD test). Error bars represent standard error of the mean (SE).

FIG. 15 shows growth rates of free-living endophytes SMCD 2204, 2206, 2208, 2210, and 2215 in vitro on potato dextrose agar (PDA) under heat stress (36° C.), drought (8% polyethylene glycol (PEG) 8000) stress and control conditions for five days and simultaneous heat (36° C.) and drought (8% PEG) for six days. Bars labeled with one or two asterisks (*) are significantly, or highly significantly, different from the same endophyte grown under control conditions (p≤0.05 or p≤0.01, respectively; ANOVA, followed by post-hoc LSD test). Error bars represent standard error of the mean (SE).

FIG. 16 shows percent germination and fresh weight of seedlings from initial experiments in which seeds were surface sterilized in 5% sodium hypochlorite for 3 min. Percent germination of wheat seeds in vitro after three days on potato dextrose agar (PDA) under heat stress (36 t), drought stress (8% polyethylene glycol (PEG) 8000) and control conditions (A, B and C) with the y axis normalized to percent germination obtained under the same conditions by seeds surface sterilized in 5% sodium hypochlorite for 1 min. Fresh weight of seedlings in vitro at seven days on PDA under heat stress, drought stress and control conditions (D, E and F). Bars labeled with one (*) or two asterisks (**) are significantly, or highly significantly, different from the no endophyte control (p≤0.05 or p≤0.01, respectively; ANOVA, followed by post-hoc LSD test). Error bars represent the standard error of the mean (SE).

FIG. 17 shows percent germination over time of wheat seeds co-cultured with the endophytes most effective at conferring abiotic stress tolerance (SMCD 2206, 2210 and 2215) compared to uncolonized, unstressed seeds (positive control) and uncolonized, stressed seeds (negative control). Energy of germination (EG) is related to the time, in days (x axis) at which 50% germination (y axis) is reached. The symbols “▪”, “x”, “∘”, “Δ”, and “□” represent the positive control, SMCD 2206 treated seeds, SMCD 2210 treated seeds, SMCD 2215 treated seeds and the negative control, respectively. Heat and drought treatments correspond to 36° C. and 8% polyethylene glycol (PEG) 8000, respectively. Error bars represent the standard error of the mean (SE). Note: The seeds used in EG determination were from the second round of experiments, and hence sterilized in 5% sodium hypochlorite for one minute, rather than three.

FIG. 18 shows the relationship between hydrothermal time (HTT) required to achieve 50% germination for heat and drought alone and 5% germination for heat and drought combined (x axis) and percent germination attained after seven days (y axis). Germination after seven days and HTT were based on the results of the second round of experiments. The symbols “▪”, “♦” and “▴” represent seeds exposed to heat (36° C.), drought (8% polyethylene glycol (PEG) 8000) or both heat and drought stress, respectively. The R-squared values associated with the trendlines are 0.96, 0.80 and 0.18 for seeds exposed to heat, drought or both heat and drought stress, respectively. Note: The seeds used to determine percent germination at seven days and HTT were from the second round of experiments, and hence treated with 5% sodium hypochlorite for one minute, rather than three.

FIG. 19 shows seeds treated or inoculated with SMCD strains demonstrate improvement in all tested seed germination parameters including seed germination vigour (SGV) efficacy.

FIG. 20 shows the relationship between drought tolerance efficiency (DTE) values in wheat (A) and barley (B) cultivars without (E−) and with (E+) endophytes, based on the average effect of symbiosis using all tested SMCD isolates, on yield exposed to drought stress in greenhouse.

FIG. 21 shows (A) endophytic (E+) inoculants (SMCD 2206, SMCD 2210, and SMCD 2215) improve kernel yield in wheat genotypes compared to control (E−) treatment (yield g/3 pots). (B) Endophytic inoculants (SMCD 2206, SMCD 2210, and SMCD 2215) improve kernel yield in two row barley (B_(a)) and six row barley (B_(b)) genotypes (kernel yield: 3 plants/pot).

FIG. 22 shows (A) Barley-six row AC Metcalfe, from left to the right: Drought (E−), Drought and SMCD 2206 (E+), Control (E−), Control and SMCD 2206 (E+); (B) Wheat-Unity cultivar, from left to the right: Drought (E−), Drought and SMCD 2215 (E+), Control (E−), Control and SMCD 2215 (E+); (C) Wheat-Verona cultivar, from left to the right: Drought (E−), Drought and SMCD 2215 (E+), Control (E−), Control and SMCD 2215 (E+); and (D) Durum wheat-TEAL, from left to the right: Drought (E−), Drought and SMCD 2210 (E+), Control (E−), Control and SMCD 2210 (E+).

FIG. 23 shows stem dry weight of (A) chickpeas, (B) lentils, and (C) peas in symbiosis with SMCD endophytes (E+) under heat stress phytotron conditions. Bars labeled with one (*) or two asterisks (**) are significantly, or highly significantly, different from the no endophyte stressed control (p≤0.05 or p≤0.01, respectively; ANOVA, followed by post-hoc LSD test).

FIG. 24 shows pods dry weight of (A) chickpeas, (B) lentils, and (C) peas in symbiosis with SMCD endophytes (E+) under heat stress phytotron conditions. Bars labeled with one (*) or two asterisks (**) are significantly, or highly significantly, different from the no endophyte stressed control (p≤0.05 or p≤0.01, respectively; ANOVA, followed by post-hoc LSD test).

FIG. 25 shows roots dry weight of (A) chickpeas, (B) lentils, and (C) peas in symbiosis with SMCD endophytes (E+) under heat stress phytotron conditions. Bars labeled with one (*) or two asterisks (**) are significantly, or highly significantly, different from the no endophyte stressed control (p≤0.05 or p≤0.01, respectively; ANOVA, followed by post-hoc LSD test).

FIG. 26 shows stem dry weight of (A) chickpeas, (B) peas, and (C) lentils under drought stress in a greenhouse. Bars labeled with one (*) or two asterisks (**) are significantly, or highly significantly, different from the no endophyte (E−) stressed control (p≤0.05 or p≤0.01, respectively; ANOVA, followed by post-hoc LSD test).

FIG. 27 shows dry weights of (A) chickpeas, (B) peas, and (C) lentils pods in association with an endophyte (E+) under drought stress in the greenhouse. Bars labeled with one (*) or two asterisks (**) are significantly different from the no endophyte (E−) stressed control (p≤0.05 or p≤0.01, respectively; ANOVA, followed by post-hoc LSD test).

FIG. 28 shows roots dry weight of (A) chickpeas, (B) peas, and (C) lentils under drought stress in the greenhouse. Bars labeled with one (*) or two asterisks (**) are significantly, or highly significantly, different from no endophyte (E−) stressed control (p≤0.05 or p≤0.01, respectively; ANOVA, followed by post-hoc LSD test).

FIG. 29 shows A. Chickpea Vanguard flowering plants bearing pods under drought stress in a greenhouse—left plant is non-symbiotic (E−) and right plant is symbiotic with strain SMCD 2215 (E+); B and C, Chickpea Vanguard plants bearing pods under drought stress in a greenhouse—(B) non-symbiotic and (C) symbiotic with SMCD 2215.

FIG. 30 shows root nodulation of pea varieties under heat stress in a phytotron: Hendel (Above) and Golden (Below) inoculated (left) and uninoculated (right) with SMCD 2215. Note: in all samples natural infection with Rhizobium sp. from pea seeds has been observed.

FIG. 31 shows SMCD2206 and SMCD 2215 considerably increase energy of seed germination (≥50%) in Glamis (lentil) as a function of time under heat and drought in vitro.

FIG. 32 shows SMCD2206 and SMCD 2215 considerably increase (energy of seed germination (≥50%) in Handel (pea) as a function of time under heat and drought in vitro.

FIG. 33 shows endophytic inoculants (SMCD 2206 and SMCD 2210) improve flax yield under drought conditions in a greenhouse. Different letters above the bars indicate statistically significant differences between samples (p<0.05, Kruskal-Wallis test).

FIG. 34 shows endophytic inoculants (SMCD 2206, SMCD 2210, and SMCD 2215) improve Canola yield under drought conditions in a greenhouse. Different letters above the bars indicate statistically significant differences between samples (p<0.05, Kruskal-Wallis test).

FIG. 35 shows the survival of wheat seeds pre-inoculated in-vitro (plates in above row) and wheat seedlings pre-inoculated in greenhouse (pots in below row) with endophytic SMCD 2206-showing healthy plant growth, and with pathogenic Fusarium avenaceum and Fusarium graminearum—showing disease symtoms and death of plants.

FIG. 36 shows Fusarium inoculants produced on wheat kernels.

FIG. 37 shows that post-emergence damping-off has been prevented by SMCD 2206 endophyte in greenhouse.

FIG. 38 shows wheat biomass (aerial a-d and root e-f) improved in the presence of SMCD 2206 endophyte compared to untreated plants. (a) control plant (E−), (b) inoculated plant (E+), (c) control flowering plant, (d) inoculated flowering plant, (e) control plant (E−, left) compared to SMCD 2206 inoculated plant (E+, right), and (f) fluorescent microscopy of SMCD 2206 wheat root-colonization (E+).

FIG. 39 shows aerial plant biomass/plant (left) and underground (root) biomass/plant (right) in control (E−) and SMCD inoculated plants (E+) against F. graminearum and F. avenaceum. Vertical error bars on data points represent the standard error of the mean.

FIG. 40 shows root length in control plant (CDC Teal) without SMCD endophyte compared to inoculated plant with SMCD strains. Bars on data points represent the standard error of the mean.

FIG. 41 shows dry weight of kernels/plant (TEAL cultivar) using the double pre-inoculation approach: a) SMCD endophyte+Fusarium avenaceum (F.av), and b) SMCD endophyte+Fusarium graminearum (F.gr). Vertical error bars on data points represent the standard error of the mean.

FIG. 42 shows comparison of TEAL spike sizes in the presence of pathogen (negative control) and without presence of pathogen (positive control). Left Figure—from left to right: i) plant+F.gr, ii) plant+F.av, and (iii) plant; Right Figure—from left to right: i) plant; ii) plant+endophyte; iii) plant+endophyte+F. av; and iv) plant+endophyte+F.gr.

FIG. 43 shows a strain specific pattern of symbiotic seed germination depicting mycovitality: Handel+6% PEG—Control (A), Handel+6% PEG+SMCD 2204 (B); Handel+6% PEG+SMCD 2204F (C), Handel+6% PEG+SMCD 2206 (D), Handel+6% PEG+SMCD 2210 (E), Handel+6% PEG+SMCD 2215 (F) after 7 d at 21° C. in darkness.

FIG. 44 shows (A) SOD and (B) MnSOD relative gene expressions in Handel exposed to PEG with and without endophytes.

FIG. 45 shows Proline relative gene expression in Handel exposed to PEG with and without endophytes.

FIG. 46 shows germination of wheat seeds in vitro after three days on potato dextrose agar (PDA). Cold stratification was imposed by keeping seeds at 4° C. cold-room for 48 hours. For endophyte-indirect and endophyte-direct treatments, seeds were germinated at approximately 4 cm distance and in direct contact respectively. A) Percentage of germination in comparison with energy of germination (50% germination). B) Efficacy of germination of wheat seeds subjected to cold and biological stratification. Efficacy was calculated by subtracting the germination percentage of control from treated seeds.

FIG. 47 shows differential expression patterns of gibberellin (TaGA3ox2 and 14-3-3) and ABA (TaNCED2 and TaABA8′OH1) genes in coleorhiza of germinating wheat seeds for three days under cold and biological stratification. Gene expression was calculated as 2^(−ΔCT).

FIG. 48 shows the ratio of expression levels (2^(−ΔCT)) of gibberellin (TaGA3ox2 and 14-3-3) and ABA (TaNCED2 and TaABA8′OH1) genes in coleorhiza of germinating wheat seeds for three days under cold and biological stratification.

FIG. 49 shows relative expression patterns of hormonal RSG and KAO regulator genes and MYB 1 and MYB 2 resistance genes in coleorhiza of germinating wheat seeds for three days under cold and biological stratification. Gene expression was calculated as 2^(−ΔCT).

FIG. 50 shows emerging radicle from wheat geminating seed (A) Inverted fluorescence (B) and fluorescence imaging of DAF-2DA fluorescence upon reaction with NO in radicle cells (C) of AC Avonlea germinant at 5 min after treatment [Nakatsubo et al. 1998] with the fungal SMCD 2206 exudate. No fluorescence reaction observed in control radicle cells. Bar=25 μm; Bar=50 μm.

FIG. 51 shows DAF-2T fluorescence intensity values at 5 min after treatment of wheat radicle from AC Avonlea germinants with the SMCD 2206 fungal exudate, fungal exudate together with the NO scavenger cPTIO, and sterile water. Radicle segments were incubated for 30 min in 2 ml of detection buffer (10 mM Tris-Hcl, pH 7.4, 10 mM KCl) containing 15 μM DAF-2DA (Sigma-Aldrich) with or without 1 mM 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO) as an NO scavenger. Average fluorescence values are reported as a ratio of the fluorescence intensity at 5 min to the fluorescence intensity at time 0. Different letters indicate statistically significant differences between samples (p<0.05, Kruskal-Wallis test).

DETAILED DESCRIPTION

Novel Strains, Compositions and Seeds

The present inventors have isolated 6 novel endophyte strains that enhance seed vitality and plant health and yield under normal and/or stressed conditions. These endophytes have been deposited as follows: International Depository Authority of Canada—IDAC (original strains deposited—IDAC, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, Canada, R3E 3R2; receipts and viability in Appendix A) and Saskatchewan Microbial Collection and Database—SMCD (copies of strains deposited) Strains:

(a) IDAC 081111-06=SMCD 2215;

(b) IDAC 081111-03=SMCD 2210;

(c) IDAC 081111-02=SMCD 2208;

(d) IDAC 081111-01=SMCD 2206;

(e) IDAC 200312-06=SMCD 2204; and

(f) IDAC 200312-05=SMCD 2204F.

Accordingly, the present disclosure provides an isolated endophyte of Streptomyces sp. strain or culture thereof which is deposited under IDAC 081111-06 or which comprises the 16S rDNA sequence as shown in SEQ ID NO:6; an isolated endophyte of Paraconyothirium sp. strain or culture thereof which is deposited as IDAC 081111-03 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:5; an isolated endophyte of Pseudeurotium sp. or culture thereof which is deposited under IDAC 081111-02 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:4; an isolated endophyte of Penicillium sp. or culture thereof which is deposited under IDAC 081111-01 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:3; an isolated culture of Cladosporium sp. which is deposited under IDAC 200312-06 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:1; and/or an isolated endophyte of Cladosporium sp. or culture thereof which is deposited under IDAC 200312-05 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:2; or combinations or mixtures thereof.

The term “endophyte” as used herein refers to a fungal or bacterial organism that can live symbiotically in a plant and is also referred to herein as “endosymbiont”. A fungal endophyte may be in the form of a spore, hypha, or mycelia. A bacterial endophyte may be a cell or group of cells. The term “endophyte” as used herein includes progeny of the strains recited herein.

Also provided herein is a composition comprising an isolated endophyte or culture disclosed herein or a combination or mixture thereof and a carrier. Typical carriers include, without limitation, an inert (non-carbon based) material used to support and deliver the densely populated active ingredient to the target, and optionally adjuvants—compounds that; promote and sustain the function of the active ingredient by protection from UV radiation; ensure rain fastness on the target; retain moisture or protect against desiccation; and/or promote the spread and dispersal of the biopesticide using standard agriculture equipments such as those disclosed by Hynes and Boyetchko (2006, Soil Biology & Biochemistry 38: 845-84).

In another embodiment, the compositions comprises at least 2, at least 3, at least 4, at least 5 or 6 of the endophyte strains or cultures disclosed herein.

Further provided herein is a seed comprising an endophyte or culture disclosed herein or a combination or mixture thereof.

In one embodiment, the seed is inoculated by soil based inoculation. In another embodiment, the seed is coated with the endophyte or culture thereof. In yet another embodiment, the seed is sprayed, injected, inoculated, grafted, coated or treated with the endophyte or culture thereof.

Methods

Further provided herein is a method of enhancing seed vitality, plant health and/or yield comprising inoculating a seed with an endophyte or culture disclosed herein or a combination or mixture thereof or with a composition disclosed herein; and cultivating a first generation plant from the seed.

The phrase “inoculating a seed” as used herein refers to applying, infecting, co-planting or coating the seed with the endophyte.

Techniques for inoculating the seed are known in the art, for example, as disclosed by Hynes and Boyetchko (2006, Soil Biology & Biochemistry 38: 845-84).

The term “enhancing seed vitality” as used herein refers to plant prenatal care improving the ability of the seed to germinate and produce a plant under normal and/or stressed conditions and includes, without limitation, any one or more of the following: breaking dormancy, providing seed stratification, increasing seed germination, modulating gene expression, decreasing time to reach energy of germination, protecting against biotic stresses, protecting against abiotic stresses, reducing hydrothermal time required for germination, increasing seed germination vigour, increasing seed germination efficacy, increasing uniformity of seed germination, ameliorating drought/heat tolerance efficacy, increasing the weight of seedlings, and increasing the yield of seedlings. Drought/Heat Tolerance Efficiency (DTE/THE) is the term opposed (antonym) to susceptibility.

Energy of germination is defined as 50% of germination, relative to the number of seeds tested. The seed germination vigour shows the difference between total percentage of germinating treated seeds and germinating untreated seeds. The hydrothermal time postulates that an individual seed begins to germinate when the sum of both temperatures and water potential are sufficiently accumulated over a period of time allowing germination. Germination efficacy is defined as the percentage of treated seeds germinating after a set time period after planting, relative to the number of seeds tested in an untreated control. Biological stratification is defined as releasing seed dormancy by a symbiont in promoting germination. Uniformity of seed germination represents the maximum percentage of seed germination within a minimal time of incubation.

The term “enhancing plant health and/or yield” as used herein refers to general improvements in the plant agricultural traits (e.g. health and productivity) of the resulting plant under normal and/or stressed conditions and includes without limitation, any one or more of the following: modulating gene expression of RSG, KAO, ABAs, GAs, 14-3-3 or NO to improve plant hormonal activities, modulating gene expression of MYBs, Pro, SOD, or MnSOD to enhance stress resistance, such as resistance to abiotic and biotic stresses, increasing the weight of the various tissues, such as root, stem, leaves and pods, increasing Rhizobium activity and nodulation frequency and improving the characteristics of the first or subsequent generation seeds, including, without limitation, any one or more of the following: subsequent generation seed weight and subsequent generation energy of germination.

Hormonal KAO, RSG, ABAs, GAs, 14-3-3 genes and primer sets are as disclosed by Zhang et al. [2007]. Stress resistance SOD, MnSOD, Pro and MYB genes and primer sets are presented in Table 6 and Table 9 (SEQ ID NO: 8-19).

The term “decreasing” or “increasing” as used herein refers to a decrease or increase in a characteristic of the endophyte treated seed or resulting plant compared to an untreated seed or resulting plant. For example, a decrease in a characteristic may be at least 5%, 10%, 15%, 25%, 50%, 75%, 100%, or 200% or more lower than the untreated control and an increase may be at least 5%, 10%, 15%, 25%, 50%, 75%, 100%, or 200% or more higher than the untreated control.

In one embodiment, the plant is cultivated under abiotic or biotic stressed conditions.

The term “abiotic stress” as used herein refers to a non-living stress that typically affects seed vitality and plant health and includes, without limitation, heat and drought stress. In one embodiment, the abiotic stress is heat stress. In another embodiment, the abiotic stress is drought stress, osmotic stress or salt stress. The term “biotic stress” as used herein refers to a living stress that typically affects seed vitality and plant health, and includes without limitation, microbial plant infections. In one embodiment, the biotic stress is a Fusarium infection.

In one embodiment, the method comprises inoculating the seed with an isolated endophyte or culture thereof of Streptomyces sp. strain which is deposited under IDAC 081111-06 or which comprises the 16S rDNA sequence as shown in SEQ ID NO:6. In an embodiment, the method increases seed germination, for decreasing time to reach energy of germination, for reducing hydrothermal time required for germination, for increasing seed germination vigour, for increasing the fresh weight of seedlings, for increasing Rhizobium activity and nodulation frequency and/or for increasing yield of seedlings. In one embodiment, the method comprises reducing the effects of stress, such as drought, heat and/or biotic stress.

In another embodiment, the method comprises inoculating the seed with an isolated endophyte or culture thereof of Paraconyothirium sp. strain which is deposited as IDAC 081111-03 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:5. In an embodiment, the method increases seed germination, decreases time to reach energy of germination, reduces hydrothermal time required for germination, increases seed germination vigour, increases the fresh weight of seedlings and/or increases yield of seedlings. In another embodiment, the method comprises reducing the effects of stress, such as drought, heat and/or biotic stress.

In yet another embodiment, the method comprises inoculating the seed with an isolated endophyte or culture thereof of Pseudeurotium sp. which is deposited under IDAC 081111-02 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:4. In an embodiment, the method decreases time to reach energy of germination, reduces hydrothermal time required for germination, increases seed germination vigour, and/or increases fresh weight of seedlings. In another embodiment, the method comprises reducing the effects of stress, such as drought and/or heat stress.

In a further embodiment, the method comprises inoculating the seed with an isolated endophyte or culture thereof of Penicillium sp. which is deposited under IDAC 081111-01 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:3. In an embodiment, the method increases seed germination, decreases time to reach energy of germination, reduces hydrothermal time required for germination, increases seed germination vigour, and/or increases yield of seedlings. In another embodiment, the method comprises reducing the effects of stress, such as drought, heat and/or biotic stress. In another embodiment, the method comprises enhancing stratification, breaking dormancy and increasing stress resistance by modulating hormonal KAO, RSG, ABAs, GAs, 14-3-3 or NO genes and/or stress resistance SOD, MnSOD, Pro or MYB gene expressions, reducing the effects of stress, such as drought, heat and/or biotic stress.

In yet a further embodiment, the method comprises inoculating the seed with an isolated endophyte or culture thereof of Cladosporium sp. which is deposited under IDAC 200312-06 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:1. In an embodiment, the method decreases time to reach energy of germination, reduces hydrothermal time required for germination, increases seed germination vigour, and/or increases the fresh weight of seedlings. In an embodiment, the method comprises reducing the effects of stress, such as drought and/or heat.

In yet another further embodiment, the method comprises inoculating the seed with an isolated endophyte or culture thereof of Cladosporium sp. which is deposited under IDAC 200312-05 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:2. In an embodiment, the method comprises reducing the effects of stress, such as drought and/or heat stress.

The term “plant” as used herein refers to a member of the Plantae Kingdom and includes all stages of the plant life cycle, including without limitation, seeds. In one embodiment, the plant is a cereal (wheat and barley), pulse (pea, lentil or chickpea), flax, or canola plant.

In an embodiment, the seed is coated with the endophyte, cultured with the endophyte or planted near the endophyte. In a particular embodiment, the seed planted near the endophyte is about 4 cm away from the endophyte.

In another aspect, there is provided a method of improving plant health and/or plant yield comprising treating plant propagation material or a plant with an endophyte or culture disclosed herein or a combination or mixture thereof or with a composition disclosed herein; and cultivating the plant propagation material into a first generation plant or allowing the plant to grow.

The term “plant propagation material” as used herein refers to any plant generative/sexual and vegetative/asexual part that has the ability to be cultivated into a new plant. In an embodiment, the plant propagation material is generative seed, generative bud or flower, and vegetative stem, cutting, root, bulb, rhizome, tuber, vegetative bud, or leaf parts.

In an embodiment, the isolated endophyte or culture thereof is an isolated endophyte of Streptomyces sp. strain or culture thereof which is deposited under the International Depositary Authority of Canada (IDAC, National Microbiology Laboratory. Public Health Agency of Canada. 1015 Arlington Street, Winnipeg, Manitoba, Canada, R3E 3R2) accession number 081111-06 or which comprises the 16S rDNA sequence as shown in SEQ ID NO:6; an isolated endophyte of Paraconyothirium sp. strain or culture thereof which is deposited as IDAC accession number 081111-03 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:5; an isolated endophyte of Pseudeurotium sp. or culture thereof which is deposited under IDAC accession number 081111-02 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:4; an isolated endophyte of Penicillium sp. or culture thereof which is deposited under IDAC accession number 081111-01 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:3; an isolated culture of Cladosporium sp. which is deposited under IDAC accession number 200312-06 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:1, and/or an isolated endophyte of Cladosporium sp. or culture thereof which is deposited under IDAC accession number 200312-05 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:2.

In another embodiment, the methods reduce the effects of stress, such as heat, drought and/or biotic stress.

In an embodiment, the methods enhance landscape development and remediation.

Accordingly, in one embodiment, there is provided a method of phytoremediation or phytoreclamation of a contaminated site comprising treating plant propagation material or a plant with an endophyte or culture disclosed herein or a combination of mixture thereof or a composition disclosed herein, and cultivating the plant propagation material into a first generation plant or allowing the plant to grow; thereby remediating or reclaiming the site.

The term “phytoremediation” as used herein refers to the use of plants for removal, reduction or neutralization of substances, wastes or hazardous material from a site so as to prevent or minimize any adverse effects on the environment. The term “phytoreclamation” as used herein refers to the use of plants for reconverting disturbed land to its former or other productive uses.

In one embodiment, the site is soil, such as at a landfill. In an embodiment, the substances, wastes or hazardous materials comprise hydrocarbons, petroleum or other chemicals, salts, or metals, such as lead, cadmium or radioisotopes.

The phrase “treating a plant propagation material or plant” as used herein refers to applying the endophyte or culture thereof alone or with any solid or liquid carrier to the plant propagation material or plant or a part of said plant. In an embodiment, treating comprises foliar application or soil application of the endophyte or combination thereof with any solid or liquid carrier at all growing stages of the plant.

The plant may be any plant. In one embodiment, the plant is a cereal (e.g. wheat or barley), pulse (e.g. pea, lentil or chickpea), flax, canola plant, coniferous tree (e.g. spruce or pine), broadleaf tree (e.g. willow or poplar), shrub (e.g. caragana or winterfat) or grass (e.g. fescue or wild rye).

The above disclosure generally describes the present application. A more complete understanding can be obtained by reference to the following specific examples. These examples are described solely for the purpose of illustration and are not intended to limit the scope of the disclosure. Changes in form and substitution of equivalents are contemplated as circumstances might suggest or render expedient. Although specific terms have been employed herein, such terms are intended in a descriptive sense and not for purposes of limitation.

The following non-limiting examples are illustrative of the present disclosure:

EXAMPLES Examples (1-14)

Dormancy and germination depend on several processes and factors. To ensure seedling establishment and success, it is important to control the underlying processes or conditions. The role of plant genetics, hormones, and different seed tissues have been relatively well studied. The present examples study the endophyte-plant seed relationship, transmitting into a root symbiotic stage towards plant maturation.

Example 1

Taxonomy

International Depository Authority of Canada—IDAC (original strains deposited) and Saskatchewan Microbial Collection and Database—SMCD (copies of strains deposited) Strains: IDAC 081111-06=SMCD 2215; IDAC 081111-03=SMCD 2210; IDAC 081111-02=SMCD 2208; IDAC 081111-01=SMCD 2206; IDAC 200312-06=SMCD 2204; IDAC 200312-05=SMCD 2204F (FIGS. 1-6 and Table 1).

SMCD 2215 strain was originally isolated as endophytic bacterium of Phyalocephala sensu lato plant endophytic SMCD fungus. Classification according to Labeda et al. [2012]. This phylogenetic study examines almost all described species (615 taxa) within the family Streptomycetaceae based on 16S rDNA gene sequences and illustrates the species diversity within this family, which is observed to contain 130 statistically supported clades.

The present 16S rDNA sequence data confirm that Streptomyces sp. strain SMCD 2215 can be assigned to a separate unknown Glade according to Labeda et al [2012] but separate species from Streptomyces lividans.

Example 2

Symbiotic Microbe-Plant Association and Level of Compatibility

The level of microbe-plant compatibility was assessed using a slightly modified method of Abdellatif et al. [2009]. In a bicompartmental agar 10 cm plate without nutrients (FIG. 7), the plant's health and the formation of root hairs—the absorbants of water and minerals—were characterized in co-culture, with and without microbial partners. In FIG. 7, the left compartment of each split plate shows a culture with the microbial partner, and the right compartment of each split plate shows a culture without the microbial partner. The experiment was repeated twice in three replicates.

As shown in the left compartment of each split plate, healthy plant tissue formed even when the plant roots were grown directly on the dense microbial mats. The biomass of root hairs is enhanced to about twice as much compared to the right compartment of each split plate where the microbial partner is absent (see left compartments).

The plant efficacy to establish symbiotic association is dependent on the type of endophyte distribution within the root endodermis. Typical endophytic root colonization is discontinuous and partial with a lower number of occupied cells<50% (Table 2) compared to the colonization of fungal pathogens which is characterized by a uniform/continual (frequency: 60-80%) colonization of cells (FIG. 8).

An endophyte's performance should not only be assessed by measuring biomass production, because what underlies the visibly increased yield is the endophyte's efficiency in colonizing the plant. This can be assessed by characterizing their association with plant cells, tissues, or organs (i.e. seed and radicles) using mathematical Indices which have been developed [Abdellatif et al. 2009] and applied in this study (FIG. 9 and FIG. 10).

These Indices are based on the following observations: Endophytic symbionts show different radicle (root)-colonization patterns (regularity or level of deviation in endophyte cell form-keg and direction-Idir when colonizing living cell) compared to dead radicle-cell (which usually remain colonized by true saprophytes).

High keg and Idir index values determine mutualistic (beneficial) plant-symbiont relationships. In conclusion, the results show that the symbiotic microbe-plant association is characterised by a high level of compatibility between the two partners, leading to an equilibrated (<50% of colonized cortex cells) and discontinuous root colonisation by the microbial endophytes measured using mathematical indices [Abdellatif et al. 2009]. This mutualistic partnership is further characterised by the direct effect of endophytic microbes on plant healthy growth (bacto- and mycodependency) when the plant is challenged to use the microbial partners as the only source of nutrients or energy for growth. In addition, the enhancement of the root hairs biomass by the endophytes was observed and measured even in roots in distal compartments of split plates where microbial partners were absent, indicating a possible systemic plant growth promoting function of the endophytes.

Example 3

Symbiotic Organs of Endophytes on Wheat

Each taxonomical group of endophytes establishes a unique type of mycovitalism, consequently forming different symbiotic organs. Characterization of the mycovitalism was done using Abdellatif et al. [2009] methodology, consisting of in vitro seed and microbe co-cultures assessing an early stage of the microbe-plant symbiotic association. The diversity of microbial symbiotic organs formed by SMCD 2204, 2206, 2210, and 2215 on wheat germinants is shown in FIG. 11.

In summary, the results show differential types of symbiotic organs formed in wheat root by each endophyte likely related to their different symbiotic functions. An equilibrated colonization abundance, patchy colonization patterns, increased hypha septation in living root cells, as well as formation of arbuscules, knots, coils and vesicles—putative symbiotic functional organs—may indicate local specialization within the fungal endophytes to promote plant mycovitality and mycoheterotrophy. Bactovitality is mostly characterized by Streptomyces intercellular curly filaments.

Symbiosis at the seed level resulted in increased wheat germinants after 10 days of co-innoculation (FIG. 12 and FIG. 13).

Example 4

Endophytes Improve Wheat Seed Germination Under Heat and Drought Stress

Seed germination is a critical life stage for plant survival and timely seedling establishment especially in stressful environments. It was hypothesized that endophytes would improve wheat seed germination under heat and drought stress. The hydrothermal time (HTT) model of germination is a conceptual model useful for predicting the timing and energy of germination (EG) under a given set of conditions. The HTT and EG are applied to determine if one or more compatible endophytes enhance heat or drought tolerance in wheat. Endophytes tested dramatically increased the percent of germination, improved EG and HTT values, and diminished wheat susceptibility to heat and drought as measured by fresh weight of seedlings. When colonised by the most effective endophyte, the values of the parameters tested in wheat seeds exposed to heat stress resembled those of unstressed seeds.

Materials and Methods

Hydrothermal Time Model of Germination and Energy of Germination

The hydrothermal time (HTT) model [Gummerson 1986] postulates that an individual seed begins to germinate when two conditions are met. First, the sum of daily temperatures, above a minimum cardinal value (T_(min)), accumulated over a period of time, must pass a threshold value (θ_(T)), measured in degree days. Second, the seed must accumulate sufficient water potential (θ_(H)) per degree-day. Thus, HTT (θ_(HT)) can be expressed as: θ_(HT)=(θ_(H))(θ_(T)).  (Equation 1)

According to Köchy and Tielbörger [2007], θ_(T)=(T _(substrate) −T _(min))t  (Equation 2) with t representing the time elapsed in days, and θ_(H)=ψ_(substrate)−ψ_(min)  (Equation 3) in a constant environment assuming that T_(substrate) is equal to or less than the optimal temperature for seed germination. In Equation 3, ψ_(substrate) and ψ_(min) represent the water potential of the substrate and the minimum water potential at which germination is possible, in MPa, respectively. Consistent with Bradford [2002], equations 2 and 3 can be substituted into equation 1 to yield: θ_(HT)=(ψ_(substrate)−ψ_(min))(T _(substrate) −T _(min))t  (Equation 4).

However, in the present study, the temperature exceeds the optimal temperature for the germination of wheat [reviewed by McMaster (2009)], necessitating the consideration of a maximum temperature (T_(max)) above which germination cannot occur. Thus, equation 2 was modified to: θ_(T)=√[(T _(substrate) −T _(min))(|T _(substrate) −T _(max)|)]t  (Equation 5) where T_(min)≤T_(substrate)≤T_(max). If equation 5 is substituted for 2 in equation 4, the following results: θ_(HT)(ψ_(substrate)−ψ_(min))√[(T _(substrate) −T _(min))(|T _(substrate) −T _(max)|)]t  (Equation 6) where T_(min)≤T_(substrate)≤T_(max).

Energy of germination (EG) can be defined in several ways, including the percentage of seeds germinating after a set time period after planting, relative to the number of seeds tested [Ruan et al. 2002; Dong-dong et al. 2009], or 50% of germination attained [Allen 1958]. In order to integrate EG with the HTT model of germination the latter definition was used, meaning that EG is equal to t in Equation 2.

Estimation of Parameters

The estimation of T_(min) and T_(max) for wheat was based on both information available in the literature and the present inventors' own observations. McMaster [2009] summarizes data originating from Friend et al. [1962], Cao and Moss [1989], and Jame et al. [1998] indicating the existence of a curvilinear relationship between wheat development rate and temperature. Since germination and development of wheat does not take place below 0° C. or above 40° C., T_(min) and T_(max) were assigned the values of 0° C. and 40° C., respectively.

The parameter ψ_(min) was estimated in vitro by germinating wheat seeds grown on potato dextrose agar (PDA; Difco) media containing a range of polyethylene glycol (PEG) 8000 concentrations (Amresco Inc.). The water activity (a_(w)) of PDA alone and PDA containing 8%, 12% and 16% PEG was measured using the AquaLab 4TE, Series 4 Quick Start, Decagon Devices. Water activity was converted to water potential (ψ) using the relationship adapted from Bloom and Richard [2002]: ψ=[(RT)ln(a _(w))]/V  (Equation 7) where R is the universal gas constant (8.314 J mol⁻¹ K⁻¹), T is the temperature in ° K, and V is the partial molar volume of water (18 mL/mol). For unit conversions, 1 J/mL=1 MPa=10 bar. Water potential is zero for a free water surface or a saturated medium; all other values are negative.

The water activities of PDA and PDA containing 8%, 12% and 16% PEG were 0.9974, 0.9890, 0.9863, and 0.9825, respectively. These values are equivalent to −0.35, −1.51, −1.88, and −2.41 MPa, respectively and are consistent with those reported in the literature [Leone et al. 1994].

Plant and Fungal Material

The plant material used was the durum wheat cultivar AC Avonlea, which has low resistance to environmental stressors [SaskSeed guide 2008]. The seeds used in the first round of experiments were produced by Paterson Grain in 2008, under field conditions, and not certified to be free of microbes. Seeds used in the second set of experiments were produced by the Agriculture and Agri-Food Canada (AAFC) Seed Increase Unit Research Farm in 2006 under greenhouse conditions, and were certified to be free of microbes. Wheat seeds were surface-sterilized with 95% ethanol for 10 s, rinsed in sterile distilled water for 10 s, submerged for either 3 min (first round of experiments involving seeds not certified to be free of microbes) or 1 min (second round of experiments using seeds certified to be microbe-free) in 5% sodium hypochlorite (Javex), rinsed three times in sterile distilled water and PDA for germination [Abdellatif et al. 2009]. A third seed sterilization method, involving a 3 hr exposure to chlorine gas (produced by combining 25 mL 6% sodium hypochlorite with 1.0 mL concentrated hydrochloric acid in a beaker) in a closed plastic box placed in a fumehood [Rivero et al. 2011] was also tested. The percent germination of seeds subjected to each sterilization protocol and placed on PDA for three days is shown in FIG. 14B. Only the 3 min submersion in sodium hypochlorite resulted in a significant decrease in germination (p≤0.01). Seed surface sterilization was intended to eliminate microbes which could compete with the endophytes being investigated. In addition, microbes present on the surface of the seeds could overgrow the plate and emerging seedling, inhibiting plant growth. All seeds used in the study were determined to be free from microorganisms after sterilization, based on the absence of unintended microbial growth on the plate.

Four endophytic Ascomycota mitosporic fungal isolates (classified according to Kiffer and Morelet [2000]): SMCD 2204, SMCD 2206, SMCD 2208, and SMCD 2210, plus the Actinomycetes filamentous gram positive bacterial isolate SMCD 2215; compatible with Triticum turgidum L. [Abdellatif et al. 2009] were used in this study. Endophytes were grown on PDA for at least three days at room temperature in darkness prior to experimental use.

Endophytes as Free-Living Organisms

Agar plugs (5 mm²) cut from the margins of the parent colony were placed in the centre of a 90-mm Petri dish containing either PDA alone or amended with 8% PEG (drought). The Petri dish was sealed with parafilm (Pechiney Plastic Packaging) to maintain sterility and placed in a bench-top incubator (Precision Thermo Scientific, model 3522) at either 23° C., or under heat stress, 36° C., in darkness. The diameter of the colony was measured at 24, 48, 72, 96 h, and five and six days. The changes in diameter were used to calculate colony growth rate. The growth of a minimum of three replicates per isolate was measured.

Endophytes Ability to Confer Heat and Drought Tolerance to Wheat

Each isolate was applied individually to wheat seeds prior to germination according to the method described in Abdellatif et al. [2010] and shown in FIG. 14A. Briefly, five surface-sterilized seeds were placed at a distance equivalent to 48-h hyphal growth from a 5 mm²-agar plug, placed hyphal side down in the centre of a 60-mm Petri dish. For slow growing isolates, the agar plug of endophyte colony was placed in the Petri dish one to four days prior to the introduction of the seeds. The seedlings were germinated for one week under abiotic stress and control conditions.

Drought stress was induced using PDA containing 8% PEG. Heat stress was induced in a bench-top incubator in darkness; the temperature was gradually raised by 2° C. every 2 h from 28° C. to 36° C. In the initial round of experiments, percent germination at three days and fresh weight at one week was assessed. Each experiment consisted of six Petri plates and was repeated, independently, three times. In subsequent experiments, percent germination was assessed every 24 hrs for seven days. Each experiment consisted of 10 Petri plates and was repeated either twice (heat and drought stress combined) or three times (heat stress, drought stress and control conditions).

The stable internal colonization of wheat roots by the intended endophytes was confirmed by re-isolation of the endophytic organism from roots which had been surface sterilized to remove an external microbial growth using a procedure modified from Larran et al. [2002]. Root fragments (˜0.5 cm) were surface sterilized in 95% ethanol for 10 s, rinsed in sterile distilled water for 10 s, submerged for 20 s in 5% sodium hypochlorite (Javex), rinsed three times in sterile distilled water and placed on PDA in a 60 mm diameter Petri dish. The Petri dish was sealed with parafilm and incubated in the dark at room temperature for four to seven days prior examination.

Statistical Analysis

The colony growth rates of free-living endophytic organisms grown under heat or drought stress were compared to those of the same organism grown under control conditions using analysis of variance (ANOVA) followed by post-hoc Fischer's' least significant difference (LSD) test. Percent germination data was subjected to arcsine transformation prior to statistical analysis [McDonald 2009]. Statistical differences between percent germination after both three and seven days, and fresh weight at seven days were assessed using a single factor ANOVA to compare all treatments. Subsequently, a post-hoc LSD test was used to evaluate the significance of differences between the no endophyte control and seeds treated with each mycobiont. The level of statistical significance associated with differences between the EG and HTT required to reach 50% germination of endophyte-colonized and control seeds were assessed by evaluating the EG for each of the three independent replicates of the experiment. The resulting data were subjected to an ANOVA and post-hoc LSD analysis. P-values less than 0.05 and 0.01 were considered to be significant and highly significant, respectively. Statistical tests were run with SPSS Inc. 2011.

Results

Within each section, the results are organised according to the type of stress: heat, drought, heat and drought, or no stress. Within each stress, the results dealing with plant material are presented according to the germinant and/or seedling traits measured: percent germination at three and seven days, fresh weight at seven days, EG and HTT.

Free-Living Endophytes

The phenotypes of SMCD 2206, 2210 and 2215 were not altered by heat (36° C.), while SMCD 2204 and 2208 did not grow at 36° C. The colony growth rates of SMCD 2206 and 2210 were reduced by 36° C. as compared to non-stressed conditions (p≤0.01), while the growth rate of SMCD 2215 at 36° C. was increased (p≤0.05) (FIG. 15). At 36° C. SMCD 2215 grew the most rapidly, followed in decreasing order by 2206 and 2210 (FIG. 15).

The morphology of SMCD 2204, 2206, 2208 and 2215 was not appreciably altered by drought (8% PEG). However, when SMCD 2210 was exposed to drought, this organism lost its “woolly” appearance and instead acquired a “shiny” or “slimy” appearance. The colony growth rates of SMCD 2204, 2206, and 2208 were reduced by drought (p≤0.01, p≤0.01, and p≤0.05 respectively), while the rate of colony growth of all other endophytes remained unchanged (FIG. 15). When drought stress was applied, SMCD 2204 grew at the highest rate followed in decreasing order by 2206, 2210, 2208 and 2215 (FIG. 15).

When challenged by 36° C. heat and drought (8% PEG) simultaneously, SMCD 2204, and 2208 failed to grow, while SMCD 2206, 2210 and 2215 grew at a significantly slower rate than under control conditions (p≤0.01) (FIG. 15). In control conditions, SMCD 2204 grew the fastest, followed in decreasing order by SMCD 2206, 2210, 2208 and 2215 (FIG. 15).

Response of Endophyte-Colonized Wheat to Heat

At 36° C., colonization by SMCD 2206 and 2215 increased germination after three days (p≤0.05 and p≤0.01, respectively; FIG. 16A), whereas SMCD 2204, 2208 and 2210 did not alter this parameter (p>0.1; FIG. 16A). After seven days, 63% and 56% of seeds germinated in co-culture with SMCD 2204 and 2208, respectively. These values were not statistically different (p>0.1) from the 59% germination achieved by the uncolonized control. In contrast, the endosymbionts SMCD 2206, 2210 and 2215 promoted germination after seven days (p≤0.01; FIG. 17).

When subjected to 36° C., the fresh weight of wheat seedlings was stable in co-culture with SMCD 2204, 2206, 2208, and 2210, while SMCD 2215 significantly increased this parameter (p≤0.01 respectively; FIG. 16D).

The EG for wheat seeds co-cultured at 36° C. with fungal endophyte SMCD 2210 (p≤0.05; Table 3, FIG. 17) improved compared to endophyte-free seeds. However, SMCD 2204, 2206, 2208 and 2215 did not alter EG (p>0.1; Table 3) relative to the control. SMCD 2210 augmented the EG to the greatest extent, followed by SMCD 2206 and 2215 (Table 3). SMCD 2210 reduced the time required for 50% of seeds to germinate to a mere two days.

When exposed to heat stress, the HTT required for germination was reduced for wheat seeds colonized by SMCD 2210 (p≤0.05; Table 3), but not any of the other endophytes tested (p>0.1; Table 3). Endophyte-free wheat seeds needed 50 MPa ° C. days more than seeds colonized by SMCD 2210 (the most effective endophyte tested) to achieve 50% germination (Table 3). There was a clear, negative, linear correlation between the HTT necessary for 50% germination and the percent germination after seven days under heat stress (FIG. 18).

Response of Endophyte-Colonized Wheat to Drought

When subjected to drought stress for three days, a diminished percentage of wheat seeds germinated in co-culture with SMCD 2208, compared to endophyte-free seeds (p≤0.01; FIG. 16B), while SMCD 2204, 2206, 2210, and 2215 did not alter this trait (p>0.1; FIG. 16B). After seven days, treatment with SMCD 2206, 2210 and 2215 led to an increase in seed germination (p≤0.01, p≤0.05, and p≤0.01, respectively; FIG. 17). In contrast, 65 and 67% of seeds co-cultured with SMCD 2204 and 2208 had germinated after seven days. Neither of these values differed statistically from the 59% of uncolonized seeds that germinated under the same conditions (p>0.1). Under drought conditions, SMCD 2208 and 2210 decreased fresh weight after seven days (p≤0.05 and p≤0.01. respectively; FIG. 16E). None of the other mycobionts altered this parameter (p>0.1; FIG. 16E).

The EG decreased for wheat seeds co-cultured in drought conditions with all endophytes tested, as compared to endophyte-free seeds (0.05<p≤0.1 for SMCD 2204 and 2208 and p≤0.05 for 2206, 2210 and 2215; Table 3). SMCD 2206 improved the EG to the greatest extent, decreasing the time elapsed before 50% germination was achieved after 2.6 days (Table 3; FIG. 17).

The HTT required for germination was reduced for wheat seeds treated with all endophytes tested under drought stress (Table 3). While uncolonized seeds needed 80 MPa ° C. days to achieve 50% germination, seeds colonized by endophyte SMCD 2206 (the most effective endophyte tested) required only 34 MPa ° C. days, representing a drop of 46 MPa ° C. days (Table 3). There was a visible, negative, linear correlation between the HTT required for 50% germination and the percent germination at seven days under drought stress (FIG. 18). However, the R² value associated with this linear relationship was smaller than for the correlation found under heat stress. The ranges of HTTs needed to achieve 50% germination differ between heat and drought stress, with values between 34 and 44 MPa ° C. days and 80 and 94 MPa ° C. days being unique to seeds exposed to drought and heat stress, respectively (FIG. 18; Table 3). The ranges of percent germination after seven days are similar between seeds exposed to drought and those subjected to heat, though the germination levels of heat-stressed seeds cover a slightly larger range (FIG. 18).

Response of Endophyte-Colonized Wheat to Drought and Heat in Combination

Very few wheat seeds germinated when exposed to drought (8% PEG) and heat stress (36° C.) simultaneously (FIG. 17). Colonization by endophytes SMCD 2210 and 2215 increased the percent germination after seven days (p≤0.01; FIG. 17). On the other hand, SMCD 2204, 2206 and 2208 failed to improve this trait (p>0.1). Seeds co-cultured with SMCD 2215 (the most beneficial microorganism tested for this parameter) reached 24% germination, four times the level attained by their endophyte-free counterparts (FIG. 17).

Because neither uncolonized seeds nor those colonized by any of the endophytes reached 50% germination within seven days, EG could not be determined and HTT was calculated for 5%, rather than 50%, germination. The time required to reach 5% germination ranged from 24 h to four days. None of the endophytes tested decreased the time required to attain 5% germination or HTT values (p>0.1). Overall, the HTT needed to reach 5% germination varied from 11 to 43 MPa ° C. days (HTT_(mean)=23.9) (FIG. 18; Table 3).

The range of HTT values for seeds subjected to both heat and drought stress were unique, as compared to the HTT values when either heat or drought was applied alone. There was a negative, linear relationship between HTT required and the percent germination under combined heat and drought stress. However, the R² value associated with this linear relationship was smaller than for the correlation found when either heat or drought stress was applied individually (FIG. 18).

Response of Endophyte-Colonized Wheat to Control Conditions

Under non-stressed conditions, SMCD 2215 significantly increased seed germination compared to uncolonized seeds after three days (p≤0.01) (FIG. 16C). SMCD 2206, 2208 and 2210 positively impacted, whereas SMCD 2204 did not alter percent of germination. In unstressed conditions, SMCD 2204, 2210 and 2215 increased the fresh weight of wheat seedlings after seven days (p≤0.05 and p≤0.01, respectively). Furthermore, SMCD 2206 and 2208 showed no impact on the fresh weight as compared to uncolonized seedlings (FIG. 16F).

In control conditions, EG and HTT parameters were slightly improved by SMCD 2206 and 2215 endosymbionts (Table 3). Relatively little alteration in EG and HTT parameters was measured associated with non-stressed wheat seeds in co-culture with different isolates.

Example 5

Endophytes Enhance Yield of Wheat and Barley Genotypes Under Severe Drought Stress

Summary:

Due to climate change and population growth, the development of techniques increasing agriculture crop tolerance in stressful environments is critical. Inoculation with three symbiotic endophytes, indigenous to the Canadian prairies, increases wheat and barley resistance to heat or drought stress, as well as grain yield and seed weight. The use of such fungal and bacterial endophytes in the field has the potential to increase the seed germination vigour (SGV=difference between total percentage of E-germinating seeds and E+ germinating seeds) (FIG. 19, FIGS. 20A and B), and to enhance yield in stress-prone conditions (Table 4; FIG. 21 A, Ba, and Bb). Evidence supports that SMCD strains increase seed-vitality and plant vigour (FIG. 22A-D). Overall results demonstrate that the prenatal care of seed using endophytic microbes, particularly SMCD strains, ensures superior crop yield of wheat and barley genotypes through physiological improvements.

Materials and Methods

Seeds of the wheat and barley cultivars were produced at University of Saskatchewan experimental plots and Crop Science Field Laboratory (Saskatoon). Visually healthy seeds were surface sterilized in 95% ethanol for 10 s, rinsed in sterile distilled water for 10 s, submerged for 1 min in 5% sodium hypochlorite (Javex) and then rinsed three times in sterile distilled water.

The endophytic isolates used in this study were originally isolated from the roots of durum wheat Triticum turgidum L. grown at field sites in Saskatchewan, Canada [Vujanovic 2007b]: SMCD 2204, 2206, 2208, 2210, 2215. All endophytic isolates are culturable on potato dextrose agar (PDA; Difco) in the absence of a host plant. Isolates were grown on PDA for three days at room temperature (23° C.) in darkness prior to experimental use.

The experiment inoculations were done in pots. Each of the endophytic isolates was applied to cereal (wheat and barley) seeds prior to germination according to the method described in Abdellatif et al. [2010]. Briefly, five surface-sterilized seeds were positioned at a distance equivalent to 48 h hyphal growth from a 5 mm² agar plug, placed hyphal side down in the centre of a 2 L plastic pot filled with 300 grams (dry weight) of autoclaved, field capacity Sunshine mix 4 potting soil. The seeds and agar plug were then covered with a 3.5-4.0 cm layer of Sunshine mix 4. Five seeds were planted per pot and there were twelve pots per treatment. Pots containing plants were placed in a greenhouse for drought stress and control treatments. The pots were arranged in a randomized block design.

Drought stress was induced from May to September when night-day maximum temperatures in the greenhouse ranged from 18 to 26° C. On sunny days, natural sunlight provided irradiation, while on cloudy or winter days with a shorter photoperiod, 1000 watt high pressure sodium light bulbs, suspended from the ceiling roughly 2 m above the plants, supplemented sunlight. In the first experiment, drought stressed and control (well watered) plants were grown at 25% soil water content by weight and 100% water retention capacity, respectively. During the experiment control plants were watered to 100% water retention capacity three times per week, while drought stressed plants were water to 100% water retention capacity weekly. This drought regime was adopted in order to mimic the natural cycle of drought that can occur during the growing season in North American prairies [Chipanshi et al. 2006].

Mature spikes were collected and dry kernels weighed on a Mettler Toledo PG802-S balance in laboratory.

Results and Discussion

Increased Wheat Seed Germination Vigour (SGV)

Under in vitro control conditions, SMCD (2204, 2206, 2208, 2210, 2215) treated wheat seeds germinated consistently faster, more uniformly, and with much higher SGE (seed germination efficacy). The SGV of seeds inoculated with SMCD (E+) was 15% to 40% greater compared to untreated (E−) seeds (FIG. 19), demonstrating SMCD's efficacy in controlling seed dormacy and enhancing seed vigor. Positive effects of SMCD strains on yield of wheat and barley genotypes under severe drought were also demonstrated.

Barley genotypes generally show higher drought susceptibility (low DTE (Drought Tolerance Efficacy) values) and lower yield performance than wheat (Table 4), possibly due to the extreme drought conditions in the greenhouse more fitting to wheat. In particular, CDC Kendall-two row barley, without endophyte (E−), shows high susceptibility to drought stress compared to other barley genotypes. However, the endophyte treatments (E+) demonstrate a remarkable positive effect on yield of all genotypes (Table 4). Conferred resistance ranges from low drought resistant CDC Kendall to highly resistant New Dale genotypes, whereas conferred resistance to wheat was consistently high.

During the maturity stage of wheat and barley, SMCD endophytes dramatically increase the genotypes drought tolerance parameters such as DTE efficacy and yield. SMCD application on Avonlea, the most drought susceptible wheat cultivar detected (DTE=16.1), resulted in a high increase in yield (77%) under drought conditions compared to control or standard watering. Carberry profited the most from endophytes under control or normal conditions, whereas CDC Utmost VB and BW 423 performed equally well under both dry and control conditions.

In conclusion, combining drought resistant genotypes with compatible endophytic SMCD 2206, SMCD 2210, and SMCD 2215 microbial symbionts maximizes plant drought resistance, an important aspect in ensuring food security. Without wishing to be bound by theory, this suggests that the most drought susceptible (low DTE values) wheat (FIG. 19A) and barley (FIG. 19B) cultivars will gain the most from the symbiotic association when exposed to the drought stress.

The only exception seemed to be the six row barley genotype Legacy showing an extremely low DTE=1.1. Although it responded positively to the endophyte presence with increased yield of 26.9% under control conditions, it ameliorated yield only for 5% in symbiosis under stress. Thus, this cultivar was excluded from the barley model presented in FIG. 19B.

Effect of Individual SMCD Strains on Wheat and Barley Productivity

Individual SMCD strains positively affect the average kernel yield of each genotype, although the actual magnitude varies by genotype-strain combination. FIG. 21 presents results obtained under drought conditions in the greenhouse (FIG. 21: A—Wheat; B_(a)—Barley (two row), and B_(b)—Barley (six row)).

Early seed contact with compatible SMCD isolates is a prerequisite for protecting crop against drought, resulting in a higher yield or production of kernels. SMCD 2206 generally confers the highest degree of improvement for most genotypes. However, strain-cultivar specificity ensures highest improvements on an individual basis, e.g. Wheat-PT580 and Barley-CDC Copeland prefer SMCD 2210; whereas Wheat-BW423 and PT580, as well as CDC Kendall show higher performance and drought resistance when inoculated with SMCD 2215.

Results highlight the importance of mycovitalism in stress-challenged wheat and barley seeds, assisting breeders in the making of highly productive cultivars capable of withstanding drought conditions significantly better than any cultivar alone (FIG. 22: A-D). Upon demonstrated performance of SMCD strains in fields, producers will have green symbiotic products to secure crop yield, and the agro-business will benefit from a guaranteed level of positive crop outcomes independent of fluctuations in environmental conditions.

Example 6

Phytotron Heat Stress Experiment on Pulses

This experiment was conducted under phytotron conditions. All seed varieties were inoculated with endophytes (SMCD 2204F, SMCD 2206, SMCD 2210, and SMCD 2215) and without endophytes in pots containing the soil mix. Details about the approaches used for endophyte inoculation on plant are described above under Example 5. Pots containing plants for heat stress were placed in a phytotron Conviron PGR15 growth chamber (Controlled Environments Ltd.) using a randomized block design. A temperature of about 33° C. was selected for heat stress. Plants were exposed to this temperature for 8 h, after which time the plants were exposed to a temperature of 21° C. for 16 h up to 10 days. After heat shock, temperatures were changed to 16° C. for 8 h and 21° C. for 16 h.

Results

In summary, the results show that the efficacy of each tested endophyte in conferring heat stress tolerance is related to the particular plant genotype or host variety (A—chickpea, B—lentil, and C—pea), and that the improvement in the biomass is associated to a particular plant organ as each organ: pod (FIG. 23), stem (FIG. 24) and root (FIG. 25), is differentially impacted by heat stress.

SMCD 2215 mostly enhanced the biomass of the stem and pod in pea, and the biomass of root in chickpea. SMCD 2206 increased the biomass of the stem and pod in lentil, and the biomass of root in chickpea, pea, and lentil. SMCD 2210 mostly improved the biomass of the stem and pod in chickpea, and the biomass of root in pea. SMCD 2204F improved the biomass of pods in most of the tested crops (chickpea, pea, and lentil). The best performer endophyte-crop genotype combination (E+) showed an improvement of about 300% in the biomass of pod, stem, and root compared to no endophyte (E−) heat stressed control.

Stem:

The following endophytes showed the best response to heat stress: Chickpea: Amit: SMCD 2210. Vanguard: SMCD 2204F; Pea: Golden: SMCD 2215. Handel: SMCD 2215; and Lentil: Glamis: SMCD 2206. Sedley: SMCD 2206.

Pods:

The following endophytes showed the best response to heat stress: Chickpea: Amit: SMCD 2210. Vanguard: SMCD 2204F; Pea: Golden: SMCD 2204F. Handel: SMCD 2215; Lentil: Glamis: SMCD 2206. Sedley: SMCD 2204F.

Root:

The following endophytes showed the best response to heat stress: Chickpea: Amit: SMCD 2215. Vanguard: SMCD 2206; SMCD 2215; Pea: Golden: SMCD 2210; SMCD2215. Handel: SMCD 2206; Lentil: Glamis: SMCD 2206; Sedley: SMCD 2204F.

Example 7

Greenhouse Drought Stress Experiment on Pulses

Six seed varieties [Amit, Vanguard (chickpeas), Golden, Handel (peas) and Glamis, Sedley (lentils)] and endophytes SMCD 2204, SMCD 2204F, SMCD 2206, SMCD 2210, and SMCD 2215 were used in this study. These experiments were conducted in the greenhouse. After sowing the seed and inoculating endophytes, pots were allowed to stay without water for 14 days to mimic severe drought as proposed by Charlton et. al. [2008] and as per the methodology and conditions outlined by Gan et al. [2004].

Results

In summary, the results show that each SMCD strain positively affects several agricultural parameters on pod production or yield (FIG. 27), and biomass of stem (FIG. 26) and root (FIG. 28) in chickpea (A), pea (B), lentil (C) and under drought stress. Overall, crop genotypes colonised by the symbiotic endophyte (E+) became more resistant to drought vs. heat stress. The level of efficacy of the tested endophytes in conferring drought tolerance varied with the particular plant organ: the pod yield was highly improved in Glamis by SMCD 2204, in Vanguard by SMCD 2204F, in Sedley by SMCD 2206, in Golden by SMCD 2210, and in Handel by SMCD 2215.

Stem:

The following endophytes showed the best response to drought stress: Chickpea: Amit: SMCD 2204F, Vanguard: SMCD 2206; Pea: Golden: SMCD 2204, Handel: SMCD 2204; SMCD 2210; SMCD 2215; Lentil: Glamis: SMCD 2204F; SMCD 2206. Sedley: SMCD 2204F; SMCD 2206.

Pods:

The following endophytes showed the best response to drought stress: Chickpea: Amit: SMCD 2204; SMCD 2210. Vanguard: SMCD 2204; SMCD 2206; SMCD 2215; Pea: Golden: SMCD 2210; SMCD2215. Handel: SMCD 2204F; SMCD 2206; SMCD 2215; Lentil: Glamis: SMCD 2204F; SMCD 2206. Sedley: SMCD 2210; SMCD2215.

Root:

The following endophytes showed the best response to drought stress: Chickpea: Amit: SMCD 2204; SMCD 2215. Vanguard: SMCD 2204F; SMCD 2206; Pea: Golden: SMCD 2204F; SMCD2215. Handel: SMCD 2204F; Lentil: Glamis: SMCD 2204F; SMCD 2206; SMCD 2210. Sedley: SMCD 2206; SMCD 2210.

Example 8

Streptomyces sp. SMCD 2215 Increases Rhizobium Activity and Nodulation Frequency in Peas Under Heat Stress

As was recently observed for another Streptomyces species, S. lydicus WYEC10 [Tokala et al. 2002], the Streptomyces sp. nov. SMCD2215 colonizes the roots of young pea seedlings from seeds produced from plants grown under control conditions. It specifically enhances plant flowering and pod yield (FIG. 29), and root nodulation by Rhizobium sp. (FIG. 30), a native endophytic colonizer of pea seeds discovered in this study (Table 5). Vegetative hyphae of Streptomyces sp. nov. SMCD2215 colonize the cells of emerging nodules as discovered by culture plate (PDA), fluorescence microscopy (Carl Zeiss Axioskop 2) and PCR (BioRad) amplification methods [Schrey and Tarkka 2008]

Example 9

Endophytes Confer Abiotic Stress Tolerance to Pulses Via Enhanced Seed Viability

Pulse crops refer to a group of more than sixty different grain legume crops grown around the world. The seeds of pulse crops are important to human nutrition. The chief constraints to pulse production are biotic and abiotic stresses such as drought, heat, cold and salinity. Recent research suggests that endophytic microbe-plant interactions are an instrumental determinant of plant adaptation.

This study hypothesizes that endophytes increase the rapidity and uniformity of seed germination under optimal and stress conditions in-vitro. The aim was, firstly, to measure the intrinsic symbiotic capacity of endophytes to trigger germination; and, secondly, to measure the efficiency of the compatible endophytes in conferring heat and drought resistance to pulses genotypes.

Material and Methods

Two varieties of pulses, Glamis (lentil) and Handel (pea), were co-cultured with compatible SMCD 2206 and SMCD 2215, fungal and bacterial symbiotic strains, respectively. The endophytic strains' ability to confer stress tolerance to Golden (FIG. 31) and Handel (FIG. 32) genotypes were tested during in-vitro seed germination modelling drought (6% PEG) and heat (33° C.) environments.

Seeds were surface sterilized with 95% ethanol for 20 s, rinsed twice in sterile distilled water for 10 s followed by 2 min in 3% sodium hypochlorite (Javex). Finally, seeds were rinsed in sterile distilled water 4 times. Seeds were inoculated on PDA media with and without endophytes in the dark at room temperature [Abdellatif et al. 2009]. Microbial organisms were grown on PDA for at least three days at room temperature in darkness prior to experimental use. The endophytic ability to confer plant stress resistance was assessed using the energy of germination, which is meant to capture the temporal nature of germination and which is defined as the number of days required to reach 50% of germinating seeds.

Results

The present study demonstrates the differential capacity of fungal or bacterial endophytes to confer drought and heat resistance in pulses specific to a fungal or bacterial strain-plant genotype-abiotic stress combination. This study used molecular and proteomic analyses to better understand the mechanism by which endophytes confer symbiotic stress resistance to pulses.

SMCD strains significantly increased the frequency of pulse seed germination under standard in-vitro conditions (FIG. 33). Under stressful conditions, both endophytes (SMCD 2206 and SMCD 2215) increased the frequency of germination when compared to non-colonized seeds. Frequency of germination was from 70-100% in symbiotic treatments and 60-80% germination in the control, meaning that the tested endophytes have the potential to increase seed germination vigour (SGV) by >15%. The highest frequency of germination (100%) was observed in Glamis (lentil) associated with both SMCD 2206 and SMCD 2215 under drought stress vs. heat stress. When co-inoculated with SMCD strains, the energy of germination (>50% germinating seeds) in Glamis was achieved in 2 days under drought and in 3 days under heat conditions. Similar results were achieved in Handel (pea), except that this genotype has inherently a higher ability to support heat shock than Glamis (lentil).

Example 10

Endophytes Enhance Yield of Flax and Canola Genotypes Under Severe Drought Stress in Greenhouse Experiment

The aim of this study was to use three randomly selected isolates (SMCD 2206, SMCD 2210 and SMCD 2215 and to expand the efficiency test on flax and canola yield production under drought stress.

Material and Methods

The experimental design, flax (Bethun and Sorel) and canola (1768S) seed manipulation, endophytic inoculant (SMCD 2206, SMCD 2210 and SMCD 2215) application, drought conditions, and yield assessment are as detailed under Example 5 with small modifications. Briefly, control plants were watered to 100% water retention capacity three times per week, while drought stressed plants were watered to 100% water retention capacity weekly. This drought regime was adopted in order to mimic the natural cycle of drought that can occur during the Canadian prairie growing season in which no precipitation falls for seven consecutive days, or more.

Results and Discussion

Severe drought conditions compromised non-symbiotic flax yield, while endophytic inoculants SMCD 2206 and SMCD 2210 dramatically improved flax yield in these same conditions. In particular, under drought conditions, SMCD 2206 maintains a nearly 100% yield in Bethun while SMCD 2210 provides a 50% yield compared to the unstressed control in the greenhouse (FIG. 34). In terms of canola, an improved yield was registered in combination with SMCD 2210 (>100%), followed by SMCD 2206 (˜50%) and SMCD 2215 (˜30%) compared with unstressed control (FIG. 35).

The bioprotection capacity was also tested in greenhouse against Fusarium avenaceum and F. graminearum. Autoclaved seeds were infected by Fusaria inoculants in darkness for 7 days at 25° C. (FIG. 36), and were inoculated by endophytes produced on petri plates as described by Abdellatif et al. [2009].

Mixed pot soil was inoculated with twenty seeds bearing Fusarium. The composition of mixed soil was 55-65% Canadian Sphagnum Peat Moss, Perlite, and Limestone mixed with sand. Standard greenhouse conditions were 8 h day light interchanged with a 16 h photoperiod (1000 lux) regime under a relative humidity of 70% and a constant temperature of 25° C.±2° C.

Plants treatments were as follows:

T1: Untreated plants (control)

T2: Plant+endophyte

T3: Plant+pathogen, Fusarium avenaceum

T4: Plant+pathogen, Fusarium graminearum

T5: Plant+endophyte fungus+Fusarium avenaceum

T6: Plant+endophyte+Fusarium graminearum

Each treatment was replicated in three pots, and seedlings were watered three times a week under controlled conditions. The endophyte-root colonisation was tested using a fluorescence microscope to distinguish symbiotic vs. pathogenic endophyte-wheat relationships [Abdellatif et al. 2009].

FIGS. 37-40 show the positive effect of endophytes on wheat post-emergency seedling resistance (FIG. 37), foliage and root biomass (FIG. 38 and FIG. 39), and flowering/anthesis stage and spikes (FIG. 38, FIG. 39, and FIG. 40). All tested endophytes induced well-developed foliage compared to control, as well as well-developed flowers in the presence of endophytes.

To confirm the ability of the endophytes to stimulate mature plant growth in the presence of Fusarium pathogens, the performance of the flowering stage bearing the spikes we assessed as a more advanced growth stage.

The histograms in FIG. 41 illustrate the performance of endophytes in improving the biomass or dry weight of wheat spikes after double inoculation (SMCD endophyte and Fusarium pathogen).

The yield of wheat in the presence of an endophyte and Fusarium significantly improves using all endophytic strains compared with treatment infected with F. graminearum and F. avenaceum but without an endophyte (E−) (FIG. 41). Plants treated with the pathogen alone show a significantly lower size of spikes compared to control plants and plants with endophytes (E+) (FIG. 42).

Example 11

Endophyte-Mediated Abiotic Stress Resistance Gene Expression in Pulses

Abstract:

The genomic and proteomic mechanisms of plant endophytes beneficial effects on host plant resistance to abiotic stressors are poorly understood. One of the contemporary theories suggests that the symbiotic plants are protected from oxidative stress produced by heat, drought and salt stressors by the production of antioxidant molecules. The aim of this study is to shed more light on defensive symbiosis of pea, chickpea and lentil genotypes assessing the Pro, SOD, and MnSOD gene expressions triggered by the association between host genotypes and endophytes. The results of this study demonstrated endophyte-mediated gene expression in endophyte-inoculated plants. These genes play an important role and provide the host protection through an enhanced stress tolerance to the tested abiotic stressors.

Materials and Methods

Leaves were collected for this analysis from normal and stressed 6 seed varieties (Amit, Vanguard [chick pea] (FIG. 43), Golden, Handel [peas] and Glamis, Sedley [lentils]) with or without endophytes.

Real-Time PCR was used to amplify genes such as Proline (Pro), SOD and Mn SOD using primers as shown in SEQ ID NOs: 8-15 (Table 6), stress proteins generally found to play special roles in protecting cytoplasm from dehydration and in protecting plants by palliating the toxicity produced by the high concentrations of ions. PCR was conducted under the following conditions: 3 min at 95° C. (enzyme activation), 40 cycles each of 30 sec at 95° C. (denaturation) and 30 s at 60° C. (anneal/extend). Finally, a melting curve analysis was performed from 65° to 95° C. in increments of 0.5° C., each lasting 5 s, to confirm the presence of a single product and absence of primer-dimer. Quantitation is relative to the control gene by subtracting the CT of the control gene from the CT of the gene of interest (ΔCT). The resulting difference in cycle number is then divided by the calibrator normalized target value, and the value obtained (ΔΔCT) is the exponent of base 2 (due to the doubling function of PCR) to generate the relative expression levels.

Results

Different gene expressions during drought stress were analyzed. Table 6 shows the genes that were tested. Some of the results obtained from Handel variety when exposed to 6% PEG.

SOD and MnSOD

In general, SODs play a major role in antioxidant defense mechanisms. In the present study very high levels of SOD expression were observed in normal (E−, control) leaves exposed to 6% PEG, an almost 200 fold increase. Endophytes played a very significant role in decreasing this stress. Especially, SMCD 2215, followed by and SMCD 2210, SMCD 2204 and SMCD 2206. These symbionts drastically reduced the stress with only a 9 and 24 fold increased expression observed (FIG. 44A).

MnSOD is one of the SOD forms. Control leaves showed a 16 fold increase in the gene expression, whereas SMCD 2215 suppressed the stress and decreased the fold change from 16 fold to 2 fold, followed by SMCD 2206, SMCD 2210 and SMCD 2204 (FIG. 44B).

Proline

Proline is essential for primary metabolism. Proline biosynthesis is controlled by the activity of two P5CS genes in plants. This gene was assessed in Pea variety Handel with endophytes under drought condition. As expected P5CS gene was upregulated and increased expression by 5 fold in the leaves collected from PEG exposed plants. Whereas the leaves collected from seeds associated with SMCD 2206 expressed 2.8 fold followed by SMCD 2215 at 3.4 fold expressed proline coding gene (FIG. 45). These results confirmed that endophytes play major role in stress resistance modifying proline gene expression compared to uninoculated stressed plants.

Example 12

Gene Expression Patterns in Wheat Coleorhiza Under Cold and Biological Stratification

Abstract:

Wheat is one of the widely used major crops in the world. However, global wheat production has decreased about 5.5% in last two decades and a further decline has been predicted due to pervasive global warming. Thus, elucidating conditions and techniques that enhance seed germination is of great importance. Cold stratification is a long-known method of releasing seed dormancy and promoting germination. Biological stratification through fungal endophytes can also stimulate seed germination in many cereal crops. Coleorhiza is one of the most active tissues in seed and it is also the first part to emerge out of germinating seeds. To evaluate the efficiency of the stratification methods, germination percentage of wheat seeds was assessed under cold and biological stratification and the expression level of gibberellin and abscisic acid genes in coleorhiza were determined. Both cold and biological stratification treatments significantly (P<0.05) enhanced the rate and efficacy of germination. Spatial distance between the fungal endophyte and seeds is a determining factor of biological stratification as seeds in direct contact with fungal endophyte showed highest germination percentage (up to 86%). High expression of GA3ox2 gene in wheat coleorhiza was found throughout the germination period revealing consistent production of the bioactive GA3 molecule. The 14-3-3 gene expression was lowest under endophyte-direct treatment. The expression of abscisic acid-ABA biosynthesis gene, TaNCED2, was considerably high in cold stratification seeds reflecting the role of abscisic acid as a stress-adaptation hormone. High expression of TaABA8′OH1 gene was also found in coleorhiza. Overall, this study provides molecular evidence of the importance of coleorhiza in germinating wheat seeds. By comparing cold and biological stratification methods, seed germinability can be markedly enhanced through application of fungal endophytes, and the spatial distance between seed and endophyte is a factor driving mycovitality.

Materials and Methods

Wheat Seeds

Seeds of the durum wheat cultivar AC Avonlea with low resistance to environmental stress conditions were used in this study. These seeds were produced by Agriculture and Agri-Food Canada Seed Increase Unit Research Farm in 2006 under greenhouse conditions, and were recommended as free of microbes. Seeds were kept in sterile ziplock bags and stored in 4° C. cold room until further use.

Comparison of Seed Sterilization Protocols

Various methods have been proposed for surface sterilization of wheat seeds. Here four widely acknowledged seed-sterilization methods were compared to identify the best suitable protocol that efficiently sterilize seed-surface without affecting seed quality and vitality in this variety of wheat. In the first method, seeds were surface sterilized with 95% ethanol for 10 s, followed by rinsing in sterile distilled water three times for 1 min [Zhang et al., 2007. BMC Genetics 8]. Second protocol was bleach-sterilization where seeds were surface sterilized in 5% sodium hypochlorite for 3 min followed by thorough rinsing in sterile distilled water three times for 1 min. In the third protocol, seeds were surface sterilized with 95% ethanol for 10 s, rinsed in sterile distilled water, then submerged for 3 min in 5% sodium hypochlorite, rinsed three times in sterile distilled water and placed on potato dextrose agar (PDA) for germination [Abdellatif et al. 2009]. The fourth method was vapour phase sterilization of seeds with chlorine gas [Desfeux et al., 2000]. In fume hood chamber, a small beaker with 20 ml bleach is placed in a 5 liter snaptite box. Wheat seeds were placed in a 96 well-plate and kept in the snaptite box. Then 3 ml of concentrated hydrochloric acid was added into the small beaker to create chlorine gas. Lid was kept closed for 4 hours to retain seeds in contact with chlorine gas. After sterilization, the 96 well-plate was placed for 1 hour in a laminar flow hood to disperse trace chlorine gas. Sterilized seeds were then rinsed three times in sterile distilled water and were plated out on PDA plates. Comparison of these sterilization methods suggests that chlorine gas sterilization protocol was the most effective method showing 80% germination without contamination while control seeds had highest percentage of contamination (Table 7). Although bleach and ethyl methods successfully inhibited contamination, seed germination was affected considerably. Therefore, chlorine gas protocol is a highly efficient method of sterilization of wheat seeds and it was selected to sterilize the seeds required for experiments conducted in this study.

Cold and Biological Stratification

For cold stratification, surface sterilized seeds were kept on moist filter paper at 4° C. cold-room for 48 hours [Mukhopadhyay et al., 2004; Wu et al., 2008]. After 2 days, cold stratified seeds were taken to room temperature where they were quickly rinsed in sterilized distilled water and placed on potato dextrose agar (PDA) plates. For biological stratification, sterilized seeds were incubated in presence of SMCD 2206. Fungal endophyte was grown on PDA at room temperature in darkness for at least three days before use. To assess this efficiency, wheat seeds were germinated in direct contact and at a certain distance from the fungal endophyte. An agar plug (5 mm²) of the endophyte dissected from the margins of a parent colony was placed in the centre of a 90 cm petri dish with PDA. Then 10 surface sterilized seeds were placed at the periphery of the petri dish encircling the fungal agar plug at approximately 4 cm distance. All petri dishes were sealed with 5 layers of Parafilm® (Pechiny Plastic Packaging) to avoid any biological contamination and diffusion of volatile/gaseous compounds. The impact of direct-contact of the fungal endophyte was elucidated by placing a 3 mm² agar plug between two adjacent surface sterilized wheat seeds and 5 mm² plug in the centre of the PDA plates. All treatments were carried out with three replicates of PDA plates with ten surface sterilized seeds on each plate. Petri dishes were incubated in a bench-top incubator at room temperature (−20° C.) in darkness. Incubation time was recorded and data collection and coleorhiza isolation were carried out after 24, 48, and 72-hours.

Germination Percentage

Emergence of early radicles was carefully monitored. Percentage of germination was calculated by estimating the number of seeds germinated out of 10 wheat seeds on each PDA plate. The 50% germination rate was assumed as the energy of germination. The efficacy of germination in different treatments was calculated by following equation: Efficacy=% germination in a treatment−% germination in control   [Eqn. 1]

Rate of germination was observed for all treated samples and replicates. For Day 2 and Day 3 samples, germination rate was monitored from Day 1 to assess the overall vitality. The PDA plates were kept sealed throughout the data collection period.

Isolation of Coleorhiza

After observing the rate of germination, PDA plates were immediately transferred to a sterile biosafety hood chamber for coleorhiza isolation. Wheat seeds were carefully dissected under compound microscope and layers of coleorhiza were cleaved off using sterilized needle and scalpel. Isolated coleorhizas were stored in an RNase-free sterilized microcentrifuge tube. Seeds from all biological replicates of a treatment were combined and approximately 20 to 30 coleorhizas were isolated to obtain optimum amount plant material for RNA extraction.

RNA Extraction and cDNA Synthesis

To avoid any degradation in plant material, RNA extraction was carried out forthwith after coleorhiza isolation on each day. Approximately 20 mg of coleorhiza samples were taken for RNA extraction. Total RNA was extracted using Aurum™ Total RNA Mini Kit according to manufacturer's instructions (Bio-Rad Laboratories). RNA concentration was spectrophotometrically measured by Nanodrop (Thermo Scientific). Immediately after RNA extraction, cDNA synthesis was performed using iScript cDNA Synthesis Kit following manufacturer's instructions (Bio-Rad Laboratories). A 600 ng aliquot of RNA was taken for cDNA synthesis. Reverse transcription was carried out at 42° C. for 30 minutes with a final denaturation at 85° C. for 5 minutes.

Quantitative Real-Time PCR

Expression of gibberellin and abscisic acid functional genes was estimated by relative quantification using quantitative real-time PCR (QRT-PCR). Various catabolic and biosynthetic genes were selected to assess their respective roles in cold and biological stratification. Wheat actin gene of 131 bp length fragment was used as the internal control [Nakamura et al., 2010]. QRT-PCR was performed using a MJ-Mini Gradient Thermal Cycler (Bio-Rad Laboratories) following manufacturer's instructions. The PCR condition was 1 cycle of 95° C. for 1 minute and 40 cycles of 94° C. for 20 s, 60° C. for 30 s, and 72° C. for 1 min. For real-time PCR, cDNA samples from the treatments were used and all reactions were carried out in three replicates and two negative controls. Each 25 μl reaction contained 18 μl of iQ™ SYBR® Green supermix (Bio-Rad Laboratories), 10 pmol of the appropriate forward and reverse primers, 2.5 μl bovine serum albumin, and 25 ng template cDNA. Relative quantification was performed according to Zhang et al. [2007]. Expression levels were calculated using cycle threshold (Ct) value determined according to manually adjusted baseline. The difference between the Ct values of target gene and actin (Ct^(target)−Ct^(actin)) was estimated as ΔCt and then the expression level was calculated as 2^(−ΔCt). The mean values of 2^(−ΔCt) were used to assess difference in expression between control and stratification treatments. To ensure the specificity and consistency of amplicons, melting curve analysis and agarose gel electrophoresis were performed after each QRT-PCR run.

Sequencing

Amplicons of Actin and various GA and ABA genes were purified using BioBasic PCR Purification Kit (Bio Basic Inc.). For each treatment, purified amplicons were sent for sequencing at Plant Biotechnology Institute (NRC-PBI). Gene sequences were identified by Basic Local Alignment Search Tool (BLAST) analyses as found at blast.ncbi.nlm.nih.gov.

Statistical Analysis

One way analysis of variance of germination percentage and gene expression data was performed using IBM SPSS Statistics software version 19. Differences between control and stratification treatments were examined with the Duncan's post-hoc test.

Results and Discussion

Percentage and Efficacy of Germination

Both cold stratification and biological stratification treatments significantly enhanced the rate of germination with all three treatments exhibiting higher germination percentage than control (FIG. 46A; Table 8). Endophyte-direct showed highest germination percentage after each day and increased 60% from Day 1 to Day 3. Throughout the germination period (3 days) it demonstrated significantly (P<0.05) higher germinability than the other three treatments. Only biological stratification treatments produced more than 50% germination after Day 2. Interestingly, endophyte-indirect treatments showed no germination after Day 1 but produced a remarkable 50% germination after Day 2. Cold stratification treatment demonstrated no significant difference from control after Day 1, and then steadily increased showing significant difference after Day 2 and Day 3. Pattern of increase in germination is also reflected in R² values. Whereas control showed an R² value of 0.40, cold stratification and endophyte-direct treatment showed 0.60 and 0.75 respectively. On the other hand, owing to its 50% increase from Day 1 to Day 2, endophyte-indirect treatment had the highest R² value of 0.93, which is about 2.5 times higher than control. Energy of germination is a critical parameter determining the capacity of seeds to break dormancy and start germination. Energy of germination is assumed as the percentage of seed germination after certain time or the number of days necessary to achieve 50% germination. Endophyte-direct showed highest efficacy followed by endophyte-indirect and cold stratification (FIG. 46B). As there was no germination in endophyte-indirect seeds after Day 1, the efficacy of germination was negative. Overall, the stratification treatments showed tremendously positive result by reaching 50% germination after 48 hours.

Stratification plays an important ecological role in the release of primary dormancy and enhancement of seed germination [Bewley and Black 1982; Probert et al., 1989]. Alleviation of seed dormancy and improvement of germination through cold stratification have been achieved in many species including grasses [Schutz and Rave 1999], mulberry [Koyuncu 2005], pine [Carpita et al., 1983], tobacco [Wu et al., 2008], rice [Mukhopadhyay et al. 2004], and apple [Bogatek and Lewak 1988]. Germination was also increased by cold stratification in 33 annual weed species and stratification has been proposed to even be capable of nullifying differences in seed germinability between populations [Milberg and Andersson 1998]. However, little information is available on the impact of cold stratification on wheat seed germination. This study found that the effect of cold stratification requires an initial period and thus seed germination was not significantly different from the control on Day 1. However, it demonstrated considerable impact on germination from Day 2 and the percentage of germination increased as much as 20% higher than the control. The time period of cold stratification in this study was selected from previous reports that showed a period of 48 hours is effective for cold stratification in tobacco [Wu et al., 2008] and rice [Mukhopadhyay et al. 2004]. Earlier studies have shown that the impact of cold stratification is proportional to its time-length [Baskin et al. 1992; Cavieres and Arroyo, 2000]. The findings support this and further extend the notion to envisage that a slightly longer stratification period (˜4 days) may be required for wheat to attain maximum germinability.

Several reports have shown the enhancement of seed germination through the application of fungal endophytes [Vujanovic 2007b; Hubbard et al. 2012; Vujanovic and Vujanovic 2007]. The present study supports the concept of “mycovitalism”, which is the increase of vitality through fungal colonization. Fungal endophytes are well known to produce volatile compounds that affect plant phenophases [Mitchell et al., 2009; Strobel et al., 2004]. Thus, endophytes may be capable of affecting seed germination even when they are not in direct contact with seeds, and this attribute is particularly useful in field conditions. Here it was also tested how physical distance may influence seed germination under biological stratification. These findings suggest that seeds in direct contact with fungal endophyte are undoubtedly more benefited than their counterparts. Endophyte-direct produced highest percentage and efficacy of seed germination on each day of the germination period. Similar to endophyte-direct contact, seeds placed at 4 cm from the endophyte also germinated at a significantly higher rate than control. However, the germination percentage and efficacy were indeed affected by the distance and indirect-contact seeds have between 14% and 27% less germination than direct-contact ones. Furthermore, no germination activity was observed on Day 1 which was followed by a sharp rise (50%) on Day 2. Seed germination is an extremely complex process and its underlying mechanisms are relatively less understood [Nonogaki et al., 2010]. Thus it is not clear how fungal endophytes facilitate the release of dormancy and onset seed germination. Considering fungi are capable of producing a range of plant-growth promoting substances, it is possible these substances are more effective in close vicinity. Consequently, endophyte-direct seeds have significantly higher germination rate than other treatments. On the contrary, endophyte-indirect seeds showed high efficacy of germination after 48 hours, this period may have allowed enough accumulation of growth promoting substances. There is a difference in germination percentage (6.6%) between the control and endophyte-indirect treatments on Day 1, however, it is not substantial.

Expression Level of Gibberellin and Abscisic Acid Genes in Coleorhiza

The GA3-oxidase 2 and 14-3-3 genes were selected as GA biosynthetic gene and negative regulator of the GA biosynthesis pathway respectively [Ji et al., 2011; Zhang et al., 2007]. The NCED gene is well known for its role in ABA biosynthesis pathway whereas ABA 8′-hydroxylase gene is involved in ABA catabolic pathway [Ji et al., 2011]. Real-time quantitative PCR analysis indicated that the differential (FIG. 47) and ratio expression (FIG. 48) values of distinct functional genes varied significantly (P<0.05) among the treatments. Except for the 14-3-3 gene on Day 3, detectable expression was observed for all four genes on each day. On Day 1, all genes were down-regulated in comparison with control. Expression of GA biosynthesis gene, TaGA3ox2, was considerably higher in cold stratification treatment than that of biological stratification. On the other hand, 14-3-3 expression did not vary significantly among cold and endophyte treatments although the expression of cold stratification was slightly higher than endophytic ones. The transcript level of ABA biosynthesis gene, TaNCED2, did not vary between control and cold stratification, and was significantly up-regulated than endophytic treatments. The ABA 8′-hydroxylase gene, TaABA8′OH1, showed significant down-regulation in all three stratification treatments, with lowest expression observed under cold stratification. The expression pattern did not vary between endophyte-indirect and endophyte-direct treatments. On Day 2, TaGA3ox2 expression was significantly down-regulated in all stratification treatments than control. Expression did not vary between cold stratification and endophyte-indirect treatments, and lowest expression was detected in endophyte-direct coleorhizas. No significant difference was observed for 14-3-3 transcript level among all four treatments, although expression was somewhat higher under cold stratification. The expression of TaNCED2 gene was significantly lower in endophytic treatments than control and cold stratification. Similarly, TaABA8′OH1 gene demonstrated considerable down-regulation in stratification treatments than control. The lowest expression was detected in endophyte-indirect treatment. The transcript level of TaGA3ox2 gene also varied significantly among the treatments on Day 3. Cold stratification showed about ten times higher expression than control while two endophytic treatments did not vary significantly. Conversely, TaNCED2 and TaABA8′OH1 genes were significantly down-regulated in all stratification treatments with lowest expression in endophyte-direct and endophyte-indirect treatments respectively. No detectable expression was observed for the 14-3-3 gene on Day 3.

The ratio of GA and ABA biosynthesis gene expression, TaGA3ox2:TaNCED2, shows no considerable difference among the treatments on Day 1 but steadily increased thereafter (FIG. 48). Endophyte-indirect exhibited highest value on Day 2, which is about 5-10 times higher than the other treatments; however, all three stratification treatments demonstrated similar values on Day 3. Conversely, for the ratio of GA biosynthesis and catabolic genes (TaGA3ox2:14-3-3), endophyte-direct showed highest value on Day 1 followed by endophyte-indirect, cold stratification, and control, which is fairly similar to their germination percentage. The ratio of GA biosynthesis and ABA catabolic genes, TaGA3ox2:TaABA1, exhibited similar patterns for all treatments on Day 1, however, endophyte-indirect was considerably higher than others on Day 2. On Day 3, cold stratification and endophyte-indirect demonstrated similar expression level and control was negligible. The ratio between ABA biosynthesis and catabolic genes (TaNCED2:TaABA1) did not vary among the treatments throughout the germination period although cold stratification showed slightly higher expression level on Day 1.

Genes encoding GA and ABA biosynthesis and catabolism enzymes show differential expression patterns depending on the accumulation of transcript [Hedden and Phillips, 2000]. Expression patterns of GA3ox1 genes have been studied in plethora of plant species including Arabidopsis [Phillips et al., 1995], rice [Oikawa et al., 2004], and wheat [Zhang et al., 2007]. Whereas other GA biosynthesis genes such as GA-20ox are associated with growing vegetative tissues, and flowers, GA3ox (GA3ox2 or GA4H) is exclusively expressed in during seed germination and supposedly plays a crucial role [Phillips et al., 1995; Yamaguchi et al., 1998; Hedden and Phillips, 2000]. Similar to previous reports, this study also demonstrated high expression of GA3ox2 gene in wheat coleorhiza throughout the germination period. Potentially, without wishing to be bound by theory, this reflects consistent production of the bioactive GA molecule GA3 in wheat coleorhiza during germination. On the other hand, the low expression of 14-3-3 gene, a negative regulator of GA biosynthesis, was also detected in coleorhiza. With gradual seedling growth and increase in endogenous GA content, the transcript level of 14-3-3 also declined and finally diminished after Day 2. Interestingly, control had highest 14-3-3 level followed by cold stratification, endophyte-indirect, and endophyte-direct, which was somewhat reflected in their germinability. These results were in accordance with previous report by Zhang et al. [2007] who showed GA biosynthesis and catabolic genes closely linked to GA content and shoot growth.

Expression patterns of the ABA pathway genes have been studied in a wide range of cereals and pulses including rice [Oliver et al., 2007], wheat [Ji et al., 2011; Nakamura et al., 2010], bean [Qin and Zeevart, 1999]. The present results show that except control and cold stratification on Day 1, expression of TaNCED2 gene did not vary among treatments. Abscisic acid plays a pivotal role in plant stress-adaptation pathways [Nakamura et al., 2010]. Since the cold stratification seeds were kept at 4° C. for 48 hours prior to their incubation at room temperature, the abscisic acid content may have been higher. On the other hand, high TaNCED2 expression in control may have resulted in higher ABA synthesis and thereby in slower germination rate. Recent reports suggest that the catabolism of ABA mainly occurs in coleorhiza [Millar et al., 2006; Okamoto et al., 2006]. Furthermore, Barrero et al. [2009] reported up-regulation and highest expression of ABA8′OH-1 in barley coleorhiza. Similar to these reports, here high expression pattern of TaABA8′OH1 gene was found in wheat coleorhiza. The ratio of GA and ABA biosynthesis genes was fairly linked to percentage of germination. Although, TaGA3ox2:TaNCED2 did not vary remarkably on Day 1, it was highest in endophyte-indirect on Day 2 owing to its significant increase. On the other hand, all three stratification treatments showed considerable up-regulation of TaGA3ox2:TaNCED2 on Day 3, which may have reflected in their germination.

The underlying mechanisms of biological stratification are still relatively unknown but they could reveal how plant-fungus interactions take place in the early stages of germination. The role of fungal endophytes as bioenhancers is widely acknowledged [Arnold et al., 2001; Hubbard et al. 2011; Saikkonen et al., 1998; Khan et al. 2012]. In this study, we demonstrated that fungal endophytes can stimulate seed germination significantly, and this mycovitality is proportional to the physical distance between the seed and fungal endophyte. Moreover, the effect of biological stratification mediated by fungal endophyte is considerably higher than cold pre-treatment. Previous studies have shown that initiation of germination is proportional to the time of cold stratification [Cavieres and Arroyo, 2000b] considering this, future study may extend cold stratification period (>48 hours) to increase seed germinability in wheat. Although, cold stratification increased the transcript level of ABA biosynthesis gene, fungal endophytes did not directly stimulate the expression of phytohormone genes in coleorhiza. However, this study specifically assessed the expression of four genes in coleorhiza.

No study has compared germination patterns under cold and biological stratification, and elucidated GA and ABA biosynthesis and catabolic gene expression in wheat coleorhiza. Coleorhiza has recently been shown as a highly active component of germinating seed [Barrero et al., 2009]. In accordance with this Example, high expression of various functional genes in coleorhiza of germinating wheat seeds was also demonstrated. Seed germinability can be substantially enhanced through the application of fungal endophytes: 1) via indirect mycovitality or without the endophyte-seed contact on tested distance (for example, the 4 cm distance was used in this Example) and 2) via direct mycovitality or once the endophyte reaches seed.

Example 13

Endophytic Stratification Effects on Hormonal Regulators (RSG and KAO) and Resistance MYBs Genes

Stratification is the exposure of seeds to cold and moist conditions in order to break dormancy, or enhance seed germination. As stratification is presently limited to the role of abiotic factors, this study aims to render the definition more inclusive by recognizing the role of biotic factors using mycovitality, or a seed-fungus symbiosis as a model. This acknowledges the existence of both cold and biological stratifications. Germination of wheat seeds subjected to cold stratification at 4° C. was compared to that of inoculated wheat seeds at room temperature. Seeds were inoculated with endophytic SMCD2206 strain. Changes in the seed's expression pattern of plant growth promoting genes—regulators (RSG and KAO) and phytohormonal gibberellins (GAs); and acquired resistance genes (MYBs) in abiotic vs. biotic conditions, during the early breakage of seed dormancy and germination, were assessed. Measurements were made in the coleorhiza cells using qRT-PCR (as described under Example 12). The results indicate that the RSG and KAO genes (FIG. 49), coding for enzymes promoting biosynthesis of GAs, and the MYBs resistance genes (FIG. 49) are up-regulated in inoculated seeds. Mycovitality, thus, demonstrates a reprogramming effect in pre- and post-germination events of wheat seed towards enhanced dormancy breakage and germination, effectively contributing to the prenatal care of cereal crops.

Material and Methods

RNA Samples

This study is the continuation of Example 12. The same material (wheat and SMCD 2206) and in vitro methods as well as the extracted RNA samples were used to assess phytohormone RSG and KAO regulators and resistance MYB gene expression by qRT-PCR.

Before RNA extraction started, tubes carried with coleorhiza tissues were stored in liquid nitrogen immediately as soon as coleorhiza tissues were isolated to preserve the cells and prevent denaturation of RNA. Aurum™ Total RNA Mini Kit (Bio-Rad Laboratories) was used in total RNA extraction from plant tissues, and it suggested a minimum 20 mg of plant tissues were suitable for each sample. The extraction steps were done rapidly and the entire process was kept either in ice, as RNA_(s) were easily denatured at room temperature. Fresh extracted total RNA_(s) were directly loaded with premixed cDNA synthesis agents obtained from iScript cDNA Synthesis Kit (Bio-Rad Laboratories). Reverse transcription was carried out at 42° C. for 30 minutes with a final denaturation at 85° C. for 5 minutes in a Thermo cycler. cDNA concentration was measured by Nanodrop spectroscopy (Thermo Scientific) and diluted or concentrated to 100 ng/μl.

Quantitative RT-PCR and Statistical Analysis

The quantitative real-time PCR (QRT-PCR) was performed on a MiniOpticon™ Real-Time PCR Detection System (Bio-Rad Laboratories) with iQTM SYBR® Green supermix kit (Bio-Rad Laboratories). In order to normalize QRT-PCR data, actin gene (131 bp length fragment) was selected as a reference gene and served as internal control to avoid fluctuation bias of gene expression under low cDNA concentration [Zhang et al. 2007; Nicot 2005]. KAO and RSG gene's primer according to Zhang et al. [2007] were tested in this experiment, whereas original primers were designed for MYB1 and MYB2 based on Triticum aestivum sequences publicly available (compbio.dfci.harvard.edu/cgi-bin/tgi/geneprod_search.pl) in Computational Biology and Functional Genomics Laboratory (Harvard University). The MBY newly designed primers (Table 9):

Transcription factor Myb2 mRNA (158 bp) which comprises the sequences as shown in SEQ ID NO:16 and SEQ ID NO:17 and transcription factor Myb1 mRNA (152 bp) which comprises the sequences as shown in SEQ ID NO:18 and SEQ ID NO: 19 (Table 9).

100 ng/μl cDNA samples were further diluted to 10 ng/μl and 2 μl cDNA were used for each 25 μl reaction. In addition, 12.5 μl of iQ™ SYBR® Green supermix, 8.5 μl sterile milli-Q water, 1 μl of each forward and reverse primer (10 pmol) were made up to 25 μl reaction mix. The protocol of thermo-cycle was suggested as 95° C. for 10 minutes and 40 cycles of 94° C. for 20 s, 60° C. for 30 s, and 72° C. for 1 min. All the cDNA samples from the treatments were carried out in three replicates and two negative controls in QRT-PCR. The gene expression levels referred to quantitative curves were carried out by CFX Manager™ Software (Bio-Rad Laboratories). Cycle quantification (Cq) value from the recorded fluorescence measurements were adjusted manually with baseline. Relative quantitation is the statistical method chosen in this study [Gizinger 2002]. Gene of interest relative to the endogenous control gene was used to compare with different treatments. The quantification (ΔCT) was done relative to the subtraction from Cq value of the gene of interest to Cq value of the control gene. ΔCT was further subtracted by calibrator value and generated corresponding ΔΔCT values which were transformed to log 2 (doubling function of PCR) to synthesize relative gene expression levels [Jurado et al., 2010]. Amplified, RSG, KAO and MYB genes were purified by using BioBasic PCR Purification Kit (Bio Basic Inc.) and sent for sequence job at Plant Biotechnology Institute (NRC-PBI). Gene sequences were identified by Basic Local Alignment Search Tool (BLAST) analyses (http://blast.ncbi.nlm.nih.gov). High identity or similar genes corresponding to different homologous organisms were assembled and aligned by software MEGA5 (Molecular Evolutionary Genetics Analysis). A phylogeny tree was made with the statistical method of Neighbor-joining based on the aligned genes.

Example 14

Nitric Oxide (NO) Showed the Regulatory Effect on Mycovitalism During Early Seed Germination Events

Nitric oxide (NO) is a highly reactive signal molecule common to fungal, animal and plant systems. NO is also known as a signaling molecule involved in eukaryotic cell hormonal signaling [Guo et al. 2003] and plant response to abiotic and biotic stresses [Hayat et al. 2010]. While there is evidence for NO accumulation, increased activation of SOD and proline contributing to the delay of O²⁻ and H₂O₂ accumulation in wheat leaves under salt stress, almost no information exists for fungal endophytes and there interaction with seed germination (mycovitalism). Here, the occurrence of NO in the early stages of germinating wheat AC Avonlea seeds was investigated for three days—endophyte SMCD 2206 on PDA, focusing on the radicle response to fungal diffusible molecules. NO was visualized in radicle (early root organ) in culture germinants by fluorescence microscopy using the specific probe 4,5-diaminofluoresce in diacetate; the assessment was conducted after five-minute of exposition to the fungal exudate, as sufficient to induce significant NO accumulation [Calcagno et al. 2012]. Since, SMCD 2206 exudate induced a significant production of NO in the wheat's root tissues; without wishing to be bound by theory, it is possible that this production is regulated by a molecular dialogue occurring in the wheat symbiosis.

Material and Methods

The accumulation of NO in radicle tissues was analyzed in wheat AC Avonlea germinating seed (in vitro approach presented under Example 12) using the cell permeable NO-specific probe DAF-2DA according to Calcagno et al. [2012] which is converted into its fluorescent triazole derivate DAF-2T upon reaction with NO. The formation of DAF-2T was visualized by fluorescence (Carl Zeiss Axioscop 2) microscopy. AC Avonlea germinant was assessed at 5 min after treatment with the fungal SMCD 2206 exudate following procedure proposed by Nakatsubo et al. [1998]

The specificity of this response to endophytic SMCD 2206 was confirmed by the lack of response in the non-inoculated radical cells. The analyses were repeated in three independent biological replicates.

Results and Discussion

Seed treatment with the fungal exudate can mimic—to some extent—the approach of endophytic hyphae during the presymbiotic phase of the interaction, as suggested for AM mycorrhiza in co-culture with Arabidopsis roots [Calcagno et al. 2010]. The fungal exudate could, therefore, be confidently used to test whether diffusible fungal signals elicit NO accumulation in the host wheat tissues (FIG. 51) during the early germination events enhancing mycovitality.

Cellular evidence, therefore, suggests that NO accumulation is a novel component in the signaling pathway that leads to mycosymbiosis related with mycovitalism of wheat seed (FIG. 51). This finding has both theoretical and practical values in attempts to improve plant prenatal-care using endophytic symbionts.

Example 15

Study of the Effects of Endophytes on Phytoremediation and Phytoreclamation

Phytoremediation is a promising environmental technique. It has been shown to be cost-effective for reclamation of hydrocarbon/petroleum, salt, heavy metal and radioisotope-contaminated soils. In this study, the effects of coniferous (Picea or Pinus) and deciduous (Salix or Populus) trees, shrubs (Caragana or Krascheninnikovia), and grasses (Festuca or Elymus) infected (E+) and non-infected (E−) by endophytic organisms (via plant propagation material, seed or root infection and colonization) (SMCD 2204, 2206, 2208, 2210 and 2215) on the decomposition, transformation or degradation of petroleum hydrocarbons in petroleum contaminated soil will be investigated. Plants will be grown in pots containing petroleum contaminated and non-contaminated soils. Plants will be inoculated and incubated for 6 months using the greenhouse method suggested by Soleimani et al. (2010). Unplanted pots will be used as control. At the end of the experiment, plant-root colonization (Abdellatif et al. 2009), soil hydrophobicity (Chau 2012), total petroleum hydrocarbons (TPHs), and polycyclic aromatic hydrocarbons (PAHs) contents will be analysed (Germida et al. 2010). The difference in E+vs. E− plants root and shoot biomass and leaf photosynthesis will be compared (Hubbard et al. 2012) with PAH and TPH removal in the rhizosphere of the plants. Unplanted pots will be used as control to calculate the efficacy of symbiotic (E+) plants on degradation of petroleum hydrocarbons (Soleimani et al. 2010). The infected plants will decompose, transform or degrade hydrocarbons and salts, uptake and accumulate and clean up or eliminate the heavy metals and radioisotopes in the contaminated site, soil or environment.

While the present disclosure has been described with reference to what are presently considered to be the examples, it is to be understood that the disclosure is not limited to the disclosed examples. To the contrary, the disclosure is intended to cover various modifications and equivalent arrangements included within the spirit and scope of the appended claims.

All publications, patents and patent applications are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety.

TABLE 1 2204 ITS rDNA CCTATAGCTGACTGCGGAGGGACATTACAAGTGACCCCGGTCTAACCAC CGGGATGTTCATAACCCTTTGTTGTCCGACTCTGTTGCCTCCGGGGCGA CCCTGCCTTCGGGCGGGGGCTCCGGGTGGACACTTCAAACTCTTGCGT AACTTTGCAGTCTGAGTAAACTTAATTAATAAATTAAAACTTTTAACAACG GATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGT AATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTG CGCCCCCTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTTCACCA CTCAAGCCTCGCTTGGTATTGGGCAACGCGGTCCGCCGCGTGCCTCAA ATCGACCGGCTGGGTCTTCTGTCCCCTAAGCGTTGTGGAAACTATTCGC TAAAGGGTGTTCGGGAGGCTACGCCGTAAAACAACCCCATTTCTAAGGT TGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAATAA GCGGAGGAAAAGAAACCAACAGGGATTGCCCCAGTAACGAA (SEQ ID NO: 1) >2204F ITS rDNA TCGATCTAGCTCATAGTGACTGCGGAGGGACATTACAAGTGACCCCGGT CTAACCACCGGGATGTTCATAACCCTTTGTTGTCCGACTCTGTTGCCTCC GGGGCGACCCTGCCTTCGGGCGGGGGCTCCGGGTGGACACTTCAAACT CTTGCGTAACTTTGCAGTCTGAGTAAACTTAATTAATAAATTAAAACTTTT AACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGC GATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACG CACATTGCGCCCCCTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCAT TTCACCACTCAAGCCTCGCTTGGTATTGGGAAACGCGGACCGACGCGTG CCTCAAATCGACCGGCAGGGTCTTCTGTCCCCTAAACGTTGTGAAAATTA TTCGATAAAGGATGTTCCGTGCTACATTGTGAATAGAACCGCATTTATAA CATTGATTATAAACTAATTACGACTACATGGTAAGATAGATATATCAAGGA ACTTCCTCTAAATGACCAAGAAACC (SEQ ID NO: 2) >2206 ITS rDNA TCGACGGCGTATCCTAGTGACTGCGGAGGATCATTACCGAGTGAGGGC CCTCTGGGTCCAACCTCCCACCCGTGTTTAATTTACCTTGTTGCTTCGGC GGGCCCGCCTTAACTGGCCGCCGGGGGGCTTACGCCCCCGGGCCCGC GCCCGCCGAAGACACCCTCGAACTCTGTCTGAAGATTGTAGTCTGAGTG AAAATATAAATTATTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCAT CGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAAATTCA GTGAATCATCGAGTCTTTGAACGCACATTGCGCCCCCTGGTATTCCGGG GGGCATGCCTGTCCGAGCGTCATTGCTGCCCTCAAGCACGGCTTGTGT GTTGGGCCCCGTCCTCCGATCCCGGGGGACGGGCCCGAAAGGCAGCG GCGGCACCGCGTCCGGTCCTCGAGCGTATGGGGCTTTGTCACCCGCTC TGTAGGCCCGGCCGGCGCTTGCCGATCAACCCAAATTTTTATCCAGGTT GACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAATAAG CGGAGGAA (SEQ ID NO: 3) >2208 ITS rDNA TAACTGATTTGGCGGACTGGCGGAAGGACATTAAAGAGACGTTGCCCTT CGGGGTATACCTCCCACCCTTTGTTTACCTTTTCCTTTGTTGCTTTGGCG GGCCCGTCCTCGGACCACCGGTTTCGGCTGGTCAGTGCCCGCCAGAGG ACCTAAAACTCTGTTTGTTCATATTGTCTGAGTACTATATAATAGTTAAAA CTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGA AATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTT GAACGCACATTGCGCCCCCTGGTATTCCGGGGGGCATGCCTGTTCGAG CGTCATTACAACCCTCAAGCTCTGCTTGGTATTGGGCTCTGCCGGTCCC GGCAGGCCTTAAAATCATTGGCGGTGCCATTCGGCTTCAAGCGTAGTAA TTCTTCTCGCTTTGGAGACCCGGGTGCGTGCTTGCCATCAACCCCCAAT TTTTTCAGGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGC ATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGTCCCAATAACG AATTTATAAATAATA (SEQ ID NO: 4) >2210 ITS rDNA TCGAGAGTTCGGACTAAGTGCCTGATCCGAGGTCAAGACGGTAATGTTG CTTCGTGGACGCGGGCCACGCCCCCCCGCAGACGCAATTGTGCTGCGC GAGAGGAGGCAAGGACCGCTGCCAATGAATTTGGGGCGAGTCCGCGCG CGAAGGCGGGACAGACGCCCAACACCAAGCAGAGCTTGAGGGTGTAGA TGACGCTCGAACAGGCATGCCCCATGGAATACCAAGGGGCGCAATGTG CGTTCAAAGATTCGATGATTCACTGAATTCTGCAATTCACACTACTTATCG CATTTCGCTGCGTTCTTCATCGATGCCAGAGCCAAGAGATCCATTGTTGA AAGTTGTAACGATTGTTTGTATCAGAACAGGTAATGCTAGATGCAAAAAA GGTTTTGTTAAGTTCCAGCGGCAGGTTGCCCCGCCGAAGGAGAACGAAA GGTGCTCGTAAAAAAAGGATGCAGGAATGCGGCGCGTGAGGGTGTTAC CCCTACCACCCGGGAGAGAACCCCCGAGGGCCGCGACCGCACCTGGTT GAGATGGATAATGATCCTTCCGCAGGTTCACCTACGGAAACC (SEQ ID NO: 5) >2215 16S rDNA CCGGGGGCACTCCACTGCGTATGTGTGACGAGTAGACCGCTGCGCTTA GCTGAGGTCTGATGAAATGTAGAACACTTAACAAAAATATGCCCGGATG GATATACTTTTCAACGACAGGGCTGCGATTGGATGATCTCCTTTGAAACA CAGAACTAGTCACGGCGACGAATACTCAACTTCGACCCCCCCCCTTTCT GGAGGCGCGTCTTAGTCCCCTCCTTGATGGAGCTGCCCCGTGCTCGGC GGCCGGAGTCGGCGGTGTTTTCCGCTGTACCTGAGACGCTGGACCAAC TCCTTCGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCT GATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCT CTTTCAGCAGGGAAGAAGCGCAAGTGACGGTACCTGCAGAAGAAGCGC CGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGCGCAAGCGT TGTCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGCTTGTCACGTCG ATTGTGAAAGCCCGAGGCTTAACCTCGGGTCTGCAGTCGATACGGGCAG GCTAGAGTGTGGTAGGGGAGATCGGAATTCCTGGTGTAGCGGTGAAAT GCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGATCTCTGGGCC ATTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGAT ACCCTGGTAGTCCACGCCGTAAACGGTGGGAACTAGGTGTTGGCGACAT TCCACGTCGTCGGTGCCGCAGCTAACGCATTAAGTTCCCCGCCTGGGG AGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCAC AAGCGGCGGAGCATGTGGCTTAATTCGACGCAACGCGAAGAACCTTACC AAGGCTTGACATACACCGGAAACATCCAGAGATGGGTGCCCCCTTGTGG TCGGCGTACAGGTCGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGT TGGGTAAGTCCCGCAACGAGCGCAACCTTGTTCTGGTGCTGCCAGCATG CCCTTCGGGTGATGGGACTTCACCACGGAGACCGCGGCTCCACTCCGA CGAGGTGGGGGACGACGTCAGTCATCATGCCCTAATGTCTGGCTG (SEQ ID NO: 6)

TABLE 2 SMCD endophytic root colonization frequency assessed in 3D wheat germinant radicles. Endophytes SMCD2204 SMCD2206 SMCD2210 SMCD2215 % 43 40 49 48 colonization

TABLE 3 Energy of germination (EG) and hydrothermal time (HTT) of wheat seeds grown under heat (36° C.), drought (potato dextrose agar (PDA) media plus 8% polyethylene glycol (PEG) 8000), heat and drought combined and control in vitro conditions. Heat Drought Heat and Drought Control HTT to 50% HTT to 50% HTT to 50% HTT to 50% germination germination germination germination EG (MPa ° C. EG (MPa ° C. EG (MPa ° C. EG (MPa ° C. Endophyte (days) days (days) days) (days) days) (days) days) SMCD 2204 3.7 ± 0.3 91 ± 7 2.9 ± 0.3  52 ± 5  2.0 ± 0.8 22 ± 8 1.6 ± 0.2 65 ± 8 SMCD 2206 2.5 ± 0.3 62 ± 7 1.9 ± 0.1 * 34 ± 2 * 2.0 ± 0.8 22 ± 8 1.5 ± 0.2 61 ± 8 SMCD 2208 3.7 ± 0.3 91 ± 7 3.0 ± 0.3  53 ± 5  4.0 ± 1.0  43 ± 10 1.6 ± 0.2 65 ± 8 SMCD 2210  1.8 ± 0.2 *  44 ± 5 * 2.2 ± 0.2 * 39 ± 3 * 1.0 ± 0.5 11 ± 5 1.6 ± 0.2 65 ± 8 SMCD 2215 2.5 ± 0.3 62 ± 7 2.3 ± 0.2 * 41 ± 3 * 1.3 ± 0.2 14 ± 2 1.5 ± 0.2 61 ± 8 No Endo 3.8 ± 0.5  94 ± 11 4.5 ± 0.5  80 ± 8  3.0 ± 1.5  32 ± 15 1.6 ± 0.2 65 ± 8 Within a column, data followed by an asterisk (*) are significantly different from the no endophyte control (p ≤ 0.05; ANOVA, followed by a post-hoc LSD test). Note: The seeds used in EG and HTT determination were from the second round of experiments, and hence subjected to sterilization in 5% sodium hypochlorite for one minute, rather than three; SMCD—Saskatchewan Microbial Collection and Database

TABLE 4 Endophytes increase drought tolerance efficiency (DTE) and yield in barley and wheat under stress conditions. Control conditions Drought Stress Average Average YIELD spikes YIELD spikes DTE^(‡) g (3plants/pot) Increased g (3plants/pot) Increased Crop Genotypes (%) E− E+ % E− E+ % WHEAT AC 16.1 18.27 25.52 28.41 2.94 10.62 72.32 Avonlea (Cont) PT 580 57.3 23.42 32.60 28.16 13.38 21.53 37.85 Control CDC 72.3 20.55 35.4 41.95 16.67 29.8 44.06 Utmost VB Strongfield 75.6 13.54 16.77* 19.26 10.23 14.98 31.71 Unity VB 75.3 20.72 26.6 22.11 15.61 23.2 32.72 CDC Teal 76.9 19.51 30.37 35.76 14.90 25.1 40.64 Carberry 83.8 17.31 33.07 47.66 14.52 22.9 36.59 BW 423 85.0 13.26 25.83 48.66 12.28 21.41 42.64 CDC 87.8 15.35 22.58 32.02 13.49 20.16 33.09 Veronna Lillian 87.8 20.50 28.3 27.56 18.1 23.6 23.31 BARLEY Two row barley CDC 4.9 6.01 10.78 44.25 2.91 6.95 58.13 Copeland CDC 13.2 9.93 24.19 58.95 0.32 1.03 68.93 Kendall AC 43.2 16.5 22.4* 26.34 7.3 14.05 48.04 Metcalfe New Dale 72.1 9.55 26.88 64.47 6.89 12.17 43.39 Six row barley Legacy 1.1 20.42 26.87* 24.00 2.26. 2.38* 5.04 CDC Bold 57.0 9.16 19.9 53.97 5.22 7.5 30.40 ^(‡)Drought tolerance efficiency (DTE) = (Yield under stress/Yield under non-stress) × 100; presented in increasing order within the Table. Genotypes with high DTE are considered as drought resistant; whereas genotypes with low DTE are considered as drought susceptible. Note: Effect of the endophyte’s absence (E−) or presence (E+) on genotype yield was calculated as an average of all three tested SMCD 2206, SMCD 2210, and SMCD 2215 strains. *Within the rows, a mean is not statistically significant at p ≥ 0.05.

TABLE 5 Rhizobium sequence maximum identity against GenBank database Max Total Query E Max Accession Description score score coverage value ident EF549401.1 Rhizobium sp. CCBAU 83431 1007 1007 46% 0.0 99% 16S ribosomal DNA gene, partial sequence Native Rhizobium nodulator in interaction with Streptomyces SMCD2215 16S F (Golden) Rhizobium sp. GGAAGGGGGGCGGCTTACCATGCAAGTCGAGCGCCCCGCAAGGGG AGCGGCAGACGGGTGAGTAACGCGTGGGAATCTACCCTTGACTACG GAATAACGCAGGGAAACTTGTGCTAATACCGTATGTGTCCTTCGGGA GAAAGATTTATCGGTCAAGGATGAGCCCGCGTTGGATTAGCTAGTTG GTGGGGTAAAGGCCTACCAAGGCGACGATCCATAGCTGGTCTGAGA GGATGATCAGCCACATTGGGACTGAGACACGGCCCAAACTCCTACG GGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCC AGCCATGCCGCGTGAGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTT CACCGGAGAAGATAATGACGGTATCCGGAGAAGAAGCCCCGGCTAA CTTCGTGCCAGCAGCCGCGGTAATACGAAGGGGGCTAGCGTTGTTC GGAATTACTGGCCGTAAAGCGCACGTAGGCGGATCGATCAGTCAGG GGTGAAATCCCAGGGCTCAACCCTGGAACTGTCTTTGATACTGTCGA TCTGGAGAACTTCCTGCTCGAGTGATTTACCCACATGGCGAGCACCG GCACCCCGTTTCGACATGCAAAAAATGATGCCCAGGCTTATGTTTGA CCTGGCTGCTACGGCTCTCTTCGGCGTGGACCCCGGCCTCCTATCC CCGGAGATGCCACCCATGGACGCCGCAGTCTCCATGGATATATCATG GAGGTGGGTTTTCTCCGACTCATGATGCCGGCTTCTTGCTGGAAGTT GATGAAGCAACTAAACATCAGCCCTGAGAGAAAGCTTCGCATGCCGC GCAGGGTGCTCCGAGTGTTCGTCTGGAGATGATGAAATAGACGAAGA TCATCTCATGTCATGTTGGTAACGACGAGAACAAGATGGTGTGGATTT TGTGTCTTCCATCCTCCATGACCCTGACGATGCTGATGATGACGTGG TTCATGCTATGATGACTCGATACTGGTCGCTGCAAGCGGATACAGTT GGGACCTACCGCTAACATGGTTCTTTCTACAACCTCCCCCCAAACCG CATAGGATCGTGGTCAATCATTCGGCACGAACCTCTTCCCCCATTGC CTCCAACTAGTTTATCGCTCTAGAGTTGGGGAGCCCTGTGTGACCTT TCGTACGCGA (SEQ ID NO: 7)

TABLE 6 Set of SOD, MnSOD and Pro primers used to assess pea [Handel] genes expression exposed to PEG drought/osmotic stress by qPCR Gene Name Primer Reference PP2A CCACATTACCTGTATCGGATGACA (F) Die et. al, Planta (2010) internal (SEQ ID NO: 8) 232:145-153 control GAGCCCAGAACAGGAGCTAACA (R) (SEQ ID NO: 9) MnSOD salt gcagaaaaaccctatcctccgtgct (F) Wong Vega et. al., Plant and drought (SEQ ID NO: 10) Mol. Biol. 17 (6), 1271- gctccaaagctccgtagtcg (R) 1274 (1991) (SEQ ID NO: 11) Pea SOD ctgtactcgctgttggggtg (F) Nakamura et. al., Plant (SEQ ID NO: 12) Biotechnol. 20, 247-253 gcatggatatggaagccgtg (R) (2003) (SEQ ID NO: 13) Proline aatggccgaaagcattgcca (F) Williamson, C.L. and (Pro) (SEQ ID NO: 14) Slocum, R.D., Plant aaggacggtgatgccgatggactc (R) Physiol. 100, 1464-1470 (SEQ ID NO: 15) (1992)

TABLE 7 Evaluation of the efficiency of seed sterilization methods. Seeds were germinated on potato dextrose agar for 4 days at ambient temperature (20° C.). Each petri dish had 10 wheat seeds. Potato dextrose agar (PDA) Sterilization type Contamination Germination Control 50% 80% 50% Bleach 0 50% 95% Ethyl alcohol 0 70% 50% Bleach + 95% 0 50% Ethyl alcohol Chlorine gas 0 80%

TABLE 8 Average germination of wheat seeds under cold and biological stratification treatments Cold Endophyte- Endophyte Day Control Stratification indirect direct 1 6.66 ± 6.66^(ab) 16.6 ± 3.33^(ab) 0.00 ± 0.00^(a) 26.6 ± 12.02^(b) 2 16.6 ± 8.81^(p) 40.0 ± 11.5^(pq) 50.0 ± 5.77^(q) 66.6 ± 8.81^(q) 3 33.3 ± 12.01^(x) 53.3 ± 8.81^(xy) 73.3 ± 3.33^(yz) 86.9 ± 7.24^(z) * Duncan test was performed to test significant difference among the treatments (Control, Cold Stratification, Endophyte-indirect, and Endophyte direct) on Day 1 (a, b, c), Day 2 (p, q), and Day 3 (x, y, z) ** Different letters indicate significant difference at P < 0.05

TABLE 9 Transcription factor Myb2 mRNA (158 bp) TaMyb2 1F acatcaagcgcggcaacttca (SEQ ID NO: 16) TaMyb2 1R gagccgcttcttgaggtgggtgt (SEQ ID NO: 17) Transcription factor Myb1 mRNA (152 bp) TaMyb1 1F ccagggaggacggacaacga (SEQ ID NO: 18) TaMyb1 1R ctctgcgccgtctcgaagga (SEQ ID NO: 19)

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The invention claimed is:
 1. A plant seed manually or mechanically coated with at least one endophyte, wherein the plant is not wheat and the endophyte is selected from the group consisting of a Streptomyces sp. strain or culture thereof which is deposited under IDAC 081111-06 or which comprises the 16S rDNA sequence as shown in SEQ ID NO:6; a Paraconiothyrium sp. strain or culture thereof which is deposited as IDAC 081111-03 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:5; a Pseudeurotium sp. or culture thereof which is deposited under IDAC 081111-02 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:4; a Penicillium sp. or culture thereof which is deposited under IDAC 081111-01 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:3; a Cladosporium sp. or culture thereof which is deposited under IDAC 200312-06 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:1; and a Cladosporium sp. or culture thereof which is deposited under IDAC 200312-05 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:2.
 2. The coated plant seed of claim 1, wherein the plant is a cereal, pulse, flax or canola plant.
 3. A method of improving seed vitality, plant health and/or yield comprising cultivating the coated plant seed of claim 1 into a first generation plant.
 4. The method of claim 3, wherein the improving seed vitality, plant health, and/or yield is for increasing seed germination, for decreasing time to reach the energy of germination, for reducing hydrothermal time required for germination, for increasing seed germination vigour, for increasing the fresh weight of seedlings, for enhancing Rhizobium nodulation traits, for increasing yield of seedlings, for reducing the effects of stress on the seed or cultivated plant, for reducing the effects of drought, heat and/or biotic stress on the seed or cultivated plant, for reducing a Fusarium infection on the seed or cultivated plant, for enhancing stratification, for breaking dormancy, for reducing the effects of stress by modulating gene expression of hormonal ent-kaurenoic (KAO), for repression of shoot growth (RSG), abscisic acid (ABA), gibberellic acid (GA), 14-3-3 genes and nitric oxide (NO) molecules, and/or for modulating gene expression of stress resistance superoxide dismutase (SOD), manganese SOD (MnSOD), proline (Pro) or MYB genes.
 5. The method of claim 3, wherein the plant is a cereal, pulse, flax, or canola plant.
 6. A method of improving plant health and/or yield comprising manually or mechanically coating a plant seed with at least one endophyte, wherein the plant is not wheat and the endophyte selected from the group consisting of a Streptomyces sp. strain or culture thereof which is deposited under IDAC 081111-06 or which comprises the 16S rDNA sequence as shown in SEQ ID NO:6; a Paraconiothyrium sp. strain or culture thereof which is deposited as IDAC 081111-03 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:5; a Pseudeurotium sp. or culture thereof which is deposited under IDAC 081111-02 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:4; a Penicillium sp. or culture thereof which is deposited under IDAC 081111-01 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:3; a Cladosporium sp. or culture thereof which is deposited under IDAC 200312-06 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:1; and a Cladosporium sp. or culture thereof which is deposited under IDAC 200312-05 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:2; and cultivating the coated plant seed into a first generation plant.
 7. The method of claim 6, wherein the improving plant health and/or yield is for reducing the effects of stress.
 8. The method of claim 6, wherein the improving plant health and/or yield is for reducing the effects of stress wherein the stress is heat, drought or biotic stress.
 9. A method of phytoremediation or phytoreclamation of a contaminated site comprising cultivating the coated plant seed of claim 1 on the site into a first generation plant; thereby remediating or reclaiming the site.
 10. The method of claim 9, wherein the site is contaminated with an organic chemical, a salt or a metal.
 11. The method of claim 9, wherein the site is contaminated with an organic chemical and the organic chemical is a hydrocarbon or a petroleum.
 12. The method of claim 9, wherein the site is contaminated with metal and the metal is lead or cadmium and/or a radioisotope.
 13. The plant seed manually or mechanically coated with at least one endophyte of claim 1, wherein the endophyte is the Streptomyces sp. strain or culture thereof which is deposited under IDAC 081111-06 or which comprises the 16S rDNA sequence as shown in SEQ ID NO:6.
 14. The plant seed manually or mechanically coated with at least one endophyte of claim 1, wherein the endophyte is the Paraconiothyrium sp. strain or culture thereof which is deposited as IDAC 081111-03 which comprises the 16S rDNA sequence as shown in SEQ ID NO:5.
 15. The plant seed manually or mechanically coated with at least one endophyte of claim 1, wherein the endophyte is the Pseudeurotium sp. or culture thereof which is deposited under IDAC 081111-02 which comprises the 16S rDNA sequence as shown in SEQ ID NO:4.
 16. The plant seed manually or mechanically coated with at least one endophyte of claim 1, wherein the endophyte is the Penicillium sp. or culture thereof which is deposited under IDAC 081111-01 which comprises the 16S rDNA sequence as shown in SEQ ID NO:3.
 17. The plant seed manually or mechanically coated with at least one endophyte of claim 1, wherein the endophyte is the Cladosporium sp. or culture thereof which is deposited under IDAC 200312-06 which comprises the 16S rDNA sequence as shown in SEQ ID NO:1.
 18. The plant seed manually or mechanically coated with at least one endophyte of claim 1, wherein the endophyte is the Cladosporium sp. or culture thereof which is deposited under IDAC 200312-05 or which comprises the ITS rDNA sequence as shown in SEQ ID NO:2. 